Difference between revisions of "Biocluster Applications"

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{| style='margin: 0 auto' class='wikitable' border='1' cellpadding='1' cellspacing='1'
 
|-
 
|-
 
!Application
 
!Application
 
!Installed Versions
 
!Installed Versions
 
!Description
 
!Description
 +
|-
 +
|[https://github.com/aidenlab/3d-dna 3d-dna]
 +
|20190801-IGB-gcc-8.2.0-Python-3.7.2
 +
|De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
 
|-
 
|-
 
|[http://454.com/products/analysis-software/index.asp 454]
 
|[http://454.com/products/analysis-software/index.asp 454]
−
|2.6, 2.7, 2.8
+
|2.8
−
|The GS Data Analysis Software package includes the tools to investigate complex genomic variation in samples including de novo assembly, reference guided alignment and variant calling, and low abundance variant identification and quantification.
+
|The GS Data Analysis Software package includes the tools to investigate complex genomic variation in samples including de novo assembly, reference guided alignment and variant calling, and low abundance variant identification and quantification. - Homepage:  http://454.com/products/analysis-software/index.asp
 
|-
 
|-
−
|[https://www.gnu.org/software/a2ps/ a2ps]
+
|[http://www-inf.enst.fr/~demaille/a2ps/ a2ps]
−
|4.14
+
|4.14-IGB-gcc-4.9.4<br>4.14-IGB-gcc-8.2.0
−
|GNU a2ps is an Any to PostScript filter. Of course it processes plain text files, but also pretty prints quite a few popular languages.
+
|a2ps-4.14: Formats an ascii file for printing on a postscript printer
 
|-
 
|-
−
|[http://omics.informatics.indiana.edu/AbundantOTU/otu+.php AbundantOTU+]
+
|[https://github.com/diyabc/abcranger abcranger]
−
|0.91b
+
|1.2.64
−
|AbundantOTU+ is the successor of AbundantOTU with additional functionality. AbundantOTU+ deals with sequences from rare species as well, compared to AbundantOTU!!
+
|Random forests methodologies for ABC model choice and ABC Bayesian parameter inference (
 
|-
 
|-
−
|[http://www.bcgsc.ca/platform/bioinfo/software/abyss abyss]
+
|[https://abseil.io/ Abseil]
−
|1.2.5, 1.3.3, 1.3.4
+
|20230125.2-IGB-gcc-8.2.0<br>20230125.3-IGB-gcc-8.2.0
 +
|Abseil is an open-source collection of C++ library code designed to augment theC++ standard library. The Abseil library code is collected from Google's ownC++ code base, has been extensively tested and used in production, and is thesame code we depend on in our daily coding lives.
 +
|-
 +
|[http://www.bcgsc.ca/platform/bioinfo/software/abyss ABySS]
 +
|2.0.2-IGB-gcc-4.9.4
 
|ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
 
|ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
 
|-
 
|-
−
|[http://standage.github.io/AEGeAn/ AEGeAn]
+
|[https://github.com/bcgsc/abyss abyss]
−
|0.14.1
+
|2.2.5-IGB-gcc-8.2.0
−
|The AEGeAn Toolkit is designed for the Analysis and Evaluation of Genome Annotations. The toolkit includes a variety of analysis programs as well as a C library whose API provides access to AEGeAn's core functions and data structures.
+
|ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.
 +
|-
 +
|[https://github.com/MikkelSchubert/adapterremoval AdapterRemoval]
 +
|2.1.7-IGB-gcc-4.9.4
 +
|This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3 end of reads following adapter removal.
 +
|-
 +
|[https://github.com/DReichLab/AdmixTools AdmixTools]
 +
|1.0.1-IGB-gcc-4.9.4
 +
|The ADMIXTOOLS package implements 5 methods described in Patterson et al. (2012) Ancient Admixture in Human History. Details of the methods and algorithm can be found in this paper.
 
|-
 
|-
−
|[http://afni.nimh.nih.gov/afni/ afni]
+
|[http://www.genetics.ucla.edu/software/admixture/index.html admixture]
−
|2011_12_21_2014
+
|1.3.0
−
|AFNI (which might be an acronym for Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.
+
|ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.  
 
|-
 
|-
−
|[http://vfsmspineagent.fsm.northwestern.edu/cgi-bin/age_nt.cgi agent]
+
|[https://projects.coin-or.org/ADOL-C ADOL-C]
−
|0.1.3
+
|2.6.3-IGB-gcc-4.9.4
−
|AGEnt performs in silico subtractive hybridization of core genome sequences, such as those produced by Spine, against a query genomic sequence to identify accessory genomic sequences (AGEs) in the query genome. Sequences are aligned using Nucmer, outputting sequences and sequence characteristics of those regions in the query genome that are not found in the core genome. If gene coordinate information is provided, a list of accessory genes in the query genome will also be provided
+
|ADOL-C is an open-source package for the automatic differentiation of C and C++ programs.
 +
|-
 +
|[https://github.com/NBISweden/AGAT AGAT]
 +
|0.5.1-IGB-gcc-8.2.0-Perl-5.28.1
 +
|Suite of tools to handle gene annotations in any GTF/GFF format.
 +
|-
 +
|[http://vfsmspineagent.fsm.northwestern.edu/ AGEnt]
 +
|0.2.1-IGB-gcc-4.9.4
 +
|AGEnt performs in silico subtractive hybridization of core genome sequences, such as those produced by Spine, against a query genomic sequence to identify accessory genomic sequences (AGEs) in the query genome. Sequences are aligned using Nucmer, outputting sequences and sequence characteristics of those regions in the query genome that are not found in the core genome. If gene coordinate information is provided, a list of accessory genes in the query genome will also be output.
 +
|-
 +
|[https://nanoporetech.com/ albacore]
 +
|2.0.2-IGB-gcc-4.9.4-Python-3.6.1<br>2.1.10-IGB-gcc-4.9.4-Python-3.6.1<br>2.3.1-IGB-gcc-4.9.4-Python-3.6.1
 +
|Local basecalling for MinKNOW
 +
|-
 +
|[https://github.com/COMBINE-lab/alevin-fry alevin-fry]
 +
|0.4.2
 +
|alevin-fry is a suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data.
 +
|-
 +
|[https://github.com/biocompibens/ALFA alfa]
 +
|1.1.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|ALFA provides a global overview of features distribution composing NGS dataset(s).
 
|-
 
|-
 
|[https://github.com/baoe/AlignGraph AlignGraph]
 
|[https://github.com/baoe/AlignGraph AlignGraph]
−
|20160714
+
|20180222-IGB-gcc-4.9.4
 
|AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
 
|AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
 
|-
 
|-
−
|[http://www.broadinstitute.org/software/allpaths-lg/blog/ allpathslg]
+
|[https://github.com/dialvarezs/alphafold alphafold]
−
|42911, 49856, 50095
+
|2.1.2<br>2.3.1<br>2.3.2
−
|ALLPATHS-LG is our original short read assembler and it works on both small and large (mammalian size) genomes. To use it, you should first generate ~100 base Illumina reads from two libraries: one from ~180 bp fragments, and one from ~3000 bp fragments, both at about 45x coverage. Sequence from longer fragments will enable longer-range continuity.
+
|This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document.
 
|-
 
|-
−
|[http://amos.sourceforge.net/wiki/index.php/AMOS amos]
+
|[http://amos.sourceforge.net/wiki/index.php/AMOS AMOS]
−
|3.1.0
+
|3.1.0-IGB-gcc-4.9.4
−
|The AMOS consortium is committed to the development of open-source whole genome assembly software
+
|The AMOS consortium is committed to the development of open-source whole genome assembly software.
 
|-
 
|-
−
|[https://github.com/martinwu/AMPHORA2 amphora]
+
|[https://github.com/martinwu/AMPHORA2 AMPHORA2]
−
|2.0
+
|20190104-IGB-gcc-4.9.4
 
|An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
 
|An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
 
|-
 
|-
−
|[https://code.google.com/p/ampliconnoise/ AmpliconNoise]
+
|[https://github.com/limey-bean/Anacapa Anacapa]
−
|1.2.7
+
|20200814-IGB-gcc-4.9.4-Python-2.7.13
−
|AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal.
+
|Anacapa is an eDNA toolkit that allows users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data.  
 
|-
 
|-
−
|[https://www.continuum.io/ anaconda2]
+
|[https://www.continuum.io/anaconda-overview Anaconda2]
−
|4.1.1
+
|4.3.1
−
|The Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. Processing multi-workload data analytics – from batch through interactive to real-time – the platform is used for both ad hoc and production deployments.
+
|Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. - Homepage: https://www.continuum.io/anaconda-overview
 
|-
 
|-
−
|[http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ ART-MountRainer]
+
|[https://www.continuum.io/anaconda-overview Anaconda3]
−
|20160605
+
|2019.10<br>2022.05<br>2023.09<br>5.0.1<br>5.1.0
−
|ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data.
+
|Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
 
|-
 
|-
−
|[http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ art]
+
|[https://github.com/ANGSD/angsd/ ANGSD]
−
|20110922
+
|0.933-IGB-gcc-4.9.4<br>0.941-IGB-gcc-8.2.0
−
|ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles.
+
|ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities.  
 
|-
 
|-
−
|[https://www.sanger.ac.uk/resources/software/artemis/ artemis]
+
|[https://ani.jgi.doe.gov/html/anicalculator.php ANIcalculator]
−
|14.0, 16.0
+
|1.0
−
|Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
+
|
 +
|-
 +
|[http://annovar.openbioinformatics.org/en/latest/ ANNOVAR]
 +
|2019Oct24-IGB-gcc-8.2.0-Perl-5.28.1
 +
|ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
 +
|-
 +
|[http://ant.apache.org/ ant]
 +
|1.10.1-Java-1.8.0_121<br>1.10.1-Java-1.8.0_152<br>1.10.10-Java-15.0.1<br>1.10.13-Java-15.0.1<br>1.10.9-Java-1.8.0_201
 +
|Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
 +
|-
 +
|[https://bitbucket.org/antismash/antismash/ antismash]
 +
|4.1.0<br>5.1.2<br>6.1.0
 +
|antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
 +
|-
 +
|ANTLR
 +
|
 +
|ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.
 
|-
 
|-
−
|[http://asperasoft.com/software/transfer-clients/connect-web-browser-plug-in/ aspera-connect]
+
|[http://merenlab.org/software/anvio/ anvio]
−
|3.5.1
+
|5.5-IGB-gcc-4.9.4-Python-3.6.1<br>6.1-IGB-gcc-4.9.4-Python-3.6.1<br>7.1-IGB-gcc-4.9.4-Python-3.6.1
−
|Aspera Connect is a self-installing web browser plug-in that powers high-speed uploads and downloads with the Aspera Connect Server, also enabling web-based transfers for Aspera web application faspexTM and Shares.
+
|Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.
 
|-
 
|-
−
|[https://github.com/smirarab/ASTRAL ASTRAL]
+
|[https://github.com/tseemann/any2fasta any2fasta]
−
|4.7.8
+
|0.4.2-IGB-gcc-8.2.0-Perl-5.28.1
−
|ASTRAL is a Java program for estimating a species tree given a set of unrooted gene trees. ASTRAL is statistically consistent under multi-species coalescent model (and thus is useful for handling ILS). It finds the tree that maximizes the number of induced quartet trees in the set of gene trees that are shared by the species tree.
+
|Convert various sequence formats to FASTA
 
|-
 
|-
−
|[http://pranjalv123.github.io/ASTRID/ ASTRID]
+
|[https://github.com/CMU-SAFARI/Apollo apollo]
−
|20151120
+
|20200510-IGB-gcc-8.2.0
−
|ASTRID is a ILS-aware tool for species tree estimation.
+
|A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
 
|-
 
|-
−
|[http://asymptote.sourceforge.net/ asymptote]
+
|[http://www.arb-home.de ARB]
−
|2.32
+
|6.0.6
−
|Asymptote is a powerful descriptive vector graphics language that provides a natural coordinate-based framework for technical drawing. Labels and equations are typeset with LaTeX, for high-quality PostScript output.
+
|The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria
 
|-
 
|-
−
|[http://math-atlas.sourceforge.net/ atlas]
+
|[https://github.com/mgbellemare/Arcade-Learning-Environment ArcadeLearningEnvironment]
−
|3.10.2
+
|0.5.1-IGB-gcc-4.9.4-Python-2.7.13
−
|The ATLAS (Automatically Tuned Linear Algebra Software) project is an ongoing research effort focusing on applying empirical techniques in order to provide portable performance. At present, it provides C and Fortran77 interfaces to a portably efficient BLAS implementation, as well as a few routines from LAPACK.
+
|The Arcade Learning Environment (ALE) -- a platform for AI research. - Homepage: https://github.com/mgbellemare/Arcade-Learning-Environment
 +
|-
 +
|[https://github.com/bcgsc/arcs ARCS]
 +
|1.0.0-IGB-gcc-4.9.4-Perl-5.24.1<br>1.2.1-IGB-gcc-8.2.0-Perl-5.28.1
 +
|Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data.
 +
|-
 +
|argtable
 +
|
 +
|Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
 +
|-
 +
|[https://aria2.github.io aria2]
 +
|1.36.0-IGB-gcc-8.2.0<br>1.37.0-IGB-gcc-8.2.0
 +
|aria2 is a lightweight multi-protocol & multi-source command-line download utility.
 +
|-
 +
|[http://cmpg.unibe.ch/software/arlequin35/Arlequin35.html Arlequin]
 +
|3.5
 +
|An Integrated Software for Population Genetics Data Analysis
 +
|-
 +
|[https://github.com/TheFraserLab/ASEr ASEr]
 +
|0.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|Get ASE counts from BAMs or raw fastq data
 +
|-
 +
|[http://asperasoft.com/ aspera]
 +
|3.7.6<br>4.2.7.445
 +
|Aspera’s unwavering mission is to create the next-generation software technologies that move the world’s data at maximum speed, regardless of file size, transfer distance and network conditions.
 +
|-
 +
|[http://assemblytics.com/ Assemblytics]
 +
|3f570cd-IGB-gcc-4.9.4<br>df5361f-IGB-gcc-4.9.4
 +
|Analyze your assembly by comparing it to a reference genome
 +
|-
 +
|[https://github.com/dfguan/asset asset]
 +
|1.0.3-IGB-gcc-8.2.0
 +
|Assembly evaluation tool
 +
|-
 +
|[http://atactk.readthedocs.io/ atactk]
 +
|0.1.6-IGB-gcc-4.9.4-Python-2.7.13
 +
|a toolkit for ATAC-seq data
 +
|-
 +
|ATK
 +
|
 +
|ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
 +
|-
 +
|[http://bioinf.uni-greifswald.de/augustus/ AUGUSTUS]
 +
|3.3-IGB-gcc-4.9.4
 +
|AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
 
|-
 
|-
 
|[http://bioinf.uni-greifswald.de/augustus/ augustus]
 
|[http://bioinf.uni-greifswald.de/augustus/ augustus]
−
|2.6.1, 3.2.1
+
|3.2.3-IGB-gcc-4.9.4<br>3.3.2-IGB-gcc-4.9.4<br>3.3.3-IGB-gcc-8.2.0<br>3.4.0-IGB-gcc-8.2.0
−
|AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
+
|AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
 +
|-
 +
|Autoconf
 +
|
 +
|Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. - Homepage: http://www.gnu.org/software/autoconf/
 
|-
 
|-
−
|[http://www.gnu.org/software/autoconf/autoconf.html autoconf]
+
|Automake
−
|2.65
+
|
−
|Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.
+
|Automake: GNU Standards-compliant Makefile generator
 +
|-
 +
|Autotools
 +
|
 +
|This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
 
|-
 
|-
−
|[http://www.gnu.org/software/automake/ automake]
+
|[https://github.com/mennthor/awkde awkde]
−
|1.15
+
|20220617-IGB-gcc-8.2.0-Python-3.7.2
−
|Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
+
|This uses the awesome pybind11 package which makes creating C++ bindings super convenient. Only the evaluation is written in a small C++ snippet to speed it up, the rest is a pure python implementation.
 
|-
 
|-
−
|[http://aws.amazon.com/cli/ awscli]
+
|[https://aws.amazon.com/cli/ awscli]
−
|1.7.36
+
|1.16.113-IGB-gcc-4.9.4-Python-3.6.1<br>1.18.96-IGB-gcc-8.2.0-Python-3.7.2
 
|The AWS Command Line Interface (CLI) is a unified tool to manage your AWS services. With just one tool to download and configure, you can control multiple AWS services from the command line and automate them through scripts.
 
|The AWS Command Line Interface (CLI) is a unified tool to manage your AWS services. With just one tool to download and configure, you can control multiple AWS services from the command line and automate them through scripts.
 
|-
 
|-
−
|[https://www.blast2go.com/ b2g4pipe]
+
|[https://github.com/genome/bam-readcount bam-readcount]
−
|2.5
+
|0.8.0-IGB-gcc-4.9.4
−
|Blast2Go without GUI frontend for command line use
+
|The purpose of this program is to generate metrics at single nucleotide positions.
 
|-
 
|-
−
|[http://www.bioinformatics.babraham.ac.uk/projects/ babraham]
+
|[http://ecogenomics.github.io/BamM/ BamM]
−
|bioinformatics
+
|1.7.3-IGB-gcc-4.9.4-Python-2.7.13
−
|Variety of projects made available by the Babraham Bioinformatics group
+
|The primary motivation for building BamM was to replaace PySam in GroopM. Not saying PySam is bad, it's just that GroopM doesn't need all the PySam features and what it does need can be done way way faster in C-land.
 
|-
 
|-
−
|[http://www.bali-phy.org/ bali-phy]
+
|[https://github.com/soedinglab/bamm-suite bamm-suite]
−
|2.1.1
+
|20191127-IGB-gcc-4.9.4-Python-3.6.1
−
|BAli-Phy is a Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward inaccurate alignment guide-trees, employs more sophisticated substitution models during alignment and automatically utilizes information in shared insertion/deletions to help infer phylogenies.
+
|BaMM-suite is the motif finding suite developed by the Soedinglab.
 
|-
 
|-
−
|[http://www.hudsonalpha.org/gsl/information/software/bam2fastq bam2fastq]
+
|[http://dna.ku.dk/%7Esapfo/bammds.html bammds]
−
|1.1.0
+
|20140602-IGB-gcc-4.9.4
−
|There are a growing number of general-purpose SAM/BAM manipulation programs, including SAMtools, Picard, and Bamtools. This tool is not intended to duplicate the complex suite of tasks those programs perform. Rather, it is simply intended to extract raw sequences (with qualities). We envision this tool being primarily useful to those wishing to duplicate or extend previous analyses.
+
|Software that allows to create a multidimensional scaling (MDS) plot of populations for genetic data.
 
|-
 
|-
−
|[http://ecogenomics.github.io/BamM/ BamM]
+
|[https://github.com/soedinglab/BaMMmotif2 BaMMmotif]
−
|20150521
+
|2.0
−
|The primary motivation for building BamM was to replaace PySam in GroopM.
+
|Bayesian Markov Model motif discovery software (version 2).
 
|-
 
|-
−
|[https://github.com/pezmaster31/bamtools bamtools]
+
|[https://github.com/pezmaster31/bamtools BamTools]
−
|0.9.0, 2.3.0, 2.4.0
+
|2.4.1-IGB-gcc-4.9.4<br>2.5.1-IGB-gcc-4.9.4<br>2.5.1-IGB-gcc-8.2.0
−
|BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.
+
|BamTools provides both a programmers API and an end-users toolkit for handling BAM files.
 
|-
 
|-
 
|[https://github.com/tseemann/barrnap barrnap]
 
|[https://github.com/tseemann/barrnap barrnap]
−
|0.5, 0.7
+
|0.9-IGB-gcc-4.9.4
−
|BAsic Rapid Ribosomal RNA Predictor
+
|Barrnap predicts the location of ribosomal RNA genes in genomes.
 +
|-
 +
|[https://github.com/zanglab/bart2 bart2]
 +
|20240302-IGB-gcc-8.2.0-Python-3.7.2
 +
|BART (Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcriptional regulators (TRs) that bind at genomic cis-regulatory regions to regulate gene expression in the human or mouse genomes, taking a query gene set, a ChIP-seq dataset or a scored genomic region set as input.
 
|-
 
|-
−
|[http://xmlgraphics.apache.org/batik/ batik]
+
|[https://developer.basespace.illumina.com/docs/content/documentation/cli/cli-overview basespace-cli]
−
|1.7
+
|1.5.1
−
|Batik is a Java-based toolkit for applications or applets that want to use images in the Scalable Vector Graphics (SVG) format for various purposes, such as display, generation or manipulation.
+
|You can work with your BaseSpace Sequence Hub data using the command line interface (CLI). The BaseSpace Sequence Hub CLI supports scripting and programmatic access to BaseSpace Sequence Hub for automation, bulk operations, and other routine functions. It can be used independently or in conjunction with BaseMount.  
 
|-
 
|-
−
|[https://bazel.build/ bazel]
+
|[https://github.com/PacificBiosciences/bax2bam bax2bam]
−
|0.4.4
+
|20171114-IGB-gcc-4.9.4
−
|Bazel is Google's own build tool, now publicly available in Beta. Bazel has built-in support for building both client and server software, including client applications for both Android and iOS platforms. It also provides an extensible framework that you can use to develop your own build rules.
+
|bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAMbasecall format.  
 +
|-
 +
|[http://cmpg.unibe.ch/software/BayeScan BayeScan]
 +
|2.1
 +
|This program, BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.  
 
|-
 
|-
−
|[https://bcbio-nextgen.readthedocs.org bcbio-nextgen]
+
|[http://bazel.io/ bazel]
−
|0.6.5
+
|0.6.0-Java-1.8.0_121
−
|A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
+
|Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Googles software.
 
|-
 
|-
−
|[http://www.htslib.org/ bcftools]
+
|[https://jgi.doe.gov/data-and-tools/bbtools/ BBMap]
−
|1.0, 1.2, 1.3.1
+
|38.36-Java-1.8.0_152<br>38.94-Java-1.8.0_201
−
|reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants
+
|BBMap short read aligner, and other bioinformatic tools.
 
|-
 
|-
−
|[http://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html bcl2fastq]
+
|[http://www.htslib.org/ BCFtools]
−
|2.17
+
|1.12-IGB-gcc-8.2.0<br>1.17-IGB-gcc-8.2.0<br>1.4-IGB-gcc-4.9.4<br>1.5-IGB-gcc-4.9.4<br>1.7-IGB-gcc-4.9.4<br>1.9-IGB-gcc-4.9.4
−
|bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
+
|BCFtools is a set of utilities that manipulate variant calls in the  Variant Call Format (VCF) and its binary counterpart BCF
 +
|-
 +
|[http://www.meilerlab.org/index.php/bclcommons/show/b_apps_id/1 bcl]
 +
|4.0.0
 +
|
 +
|-
 +
|[https://support.illumina.com/downloads/bcl2fastq-conversion-software-v2-20.html bcl2fastq2]
 +
|2.20<br>2.20-IGB-gcc-8.2.0
 +
|The bcl2fastq2 Conversion Software v2.20.0 can be used to convert BCL files from MiniSeq, MiSeq, NextSeq, HiSeq, and NovaSeq sequening systems. For conversion of data generated on Illumina sequencing systems using versions of RTA earlier than RTA 1.18.54, use bcl2fastq v1.8.4.
 
|-
 
|-
 
|[https://faculty.washington.edu/browning/beagle/beagle.html beagle]
 
|[https://faculty.washington.edu/browning/beagle/beagle.html beagle]
−
|4.1
+
|03Jul18.40b-Java-1.8.0_152<br>5.1-Java-1.8.0_152
−
|Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
+
|Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Version 5.0 has new, fast algorithms for genotype phasing and imputation.
 +
|-
 +
|[https://github.com/beagle-dev/beagle-lib beagle-lib]
 +
|4.0.0-IGB-gcc-8.2.0
 +
|BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.
 +
|-
 +
|[https://www.beast2.org/ BEAST2]
 +
|2.7.5-IGB-gcc-8.2.0
 +
|BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models.
 +
|-
 +
|[https://www.beast2.org/ beast2]
 +
|2.6.7-Java-1.8.0_201
 +
|BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models.
 +
|-
 +
|[https://bedops.readthedocs.io/en/latest/ bedops]
 +
|2.4.30
 +
|BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
 +
|-
 +
|[https://github.com/arq5x/bedtools2 BEDTools]
 +
|2.21.0-IGB-gcc-4.9.4<br>2.26.0-IGB-gcc-4.9.4<br>2.28.0-IGB-gcc-8.2.0
 +
|The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
 +
|-
 +
|[https://github.com/pmelsted/bifrost Bifrost]
 +
|1.0.4-IGB-gcc-8.2.0
 +
|Parallel construction, indexing and querying of colored and compacted de Bruijn graphs
 +
|-
 +
|[https://github.com/HAugustijn/BiG-MAP2 big-map2-analyse]
 +
|20200124
 +
|This is the Github repository for the Biosynthetic Gene cluster Meta’omics abundance Profiler
 +
|-
 +
|[https://github.com/HAugustijn/BiG-MAP2 big-map2-process]
 +
|20200124
 +
|This is the Github repository for the Biosynthetic Gene cluster Meta’omics abundance Profiler
 
|-
 
|-
−
|[http://www.beast2.org/ beast]
+
|[https://git.wageningenur.nl/medema-group/BiG-SCAPE BiG-SCAPE]
−
|2.1.3
+
|1.0.1-IGB-gcc-4.9.4-Python-3.6.1<br>1.1.5-IGB-gcc-8.2.0-Python-3.7.2
−
|Bayesian evolutionary analysis by sampling trees
+
|BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs)
 
|-
 
|-
−
|[http://bedops.readthedocs.org/en/latest/ bedops]
+
|binutils
−
|2.4.2
+
|
−
|BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
+
|binutils: GNU binary utilities
 
|-
 
|-
−
|[https://github.com/arq5x/bedtools2 bedtools]
+
|[https://github.com/sacdallago/bio_embeddings bio-embeddings]
−
|2.10.0, 2.10.1, 2.17.0, 2.20.1, 2.21.0, 2.24.0, 2.25.0
+
|0.2.2-IGB-gcc-8.2.0-Python-3.7.2
−
|Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
+
|Quickly predict protein structure and function from sequence via embeddings:
 
|-
 
|-
−
|[http://cistrome.org/BETA/index.html BETA]
+
|[https://github.com/lmrodriguezr/rocker bio-rocker]
−
|1.0.7
+
|1.2.0-IGB-gcc-4.9.4-Ruby-2.4.2
−
|Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
+
|Accurately detecting functional genes in metagenomes.
 
|-
 
|-
−
|[http://biodatabase.igb.illinois.edu biodatabase]
+
|[https://github.com/lh3/bioawk bioawk]
−
|1.1
+
|1.0-IGB-gcc-8.2.0
−
|Scripts to create, delete, and manage mysql databases on IGB's biodatabase server
+
|Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
 +
|-
 +
|[https://github.com/IGBIllinois/biodatabase/ biodatabase]
 +
|1.0-IGB-gcc-4.9.4
 +
|Scripts to create databases on the biodatabase machine.
 
|-
 
|-
 
|[http://biom-format.org/ biom-format]
 
|[http://biom-format.org/ biom-format]
−
|2.1.5
+
|2.1.6-IGB-gcc-4.9.4-Python-2.7.13<br>2.1.6-IGB-gcc-4.9.4-Python-3.6.1<br>2.1.8-IGB-gcc-4.9.4-Python-3.6.1<br>2.1.8-IGB-gcc-8.2.0-Python-3.7.2
−
|The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.
+
|The BIOM file format (canonically pronounced biome) is designed to be a general-useformat for representing biological sample by observation contingency tables.
 
|-
 
|-
−
|[http://www.bioperl.org/wiki/Main_Page bioperl]
+
|[http://www.bioperl.org/ BioPerl]
−
|1.6.924
+
|1.7.1-IGB-gcc-4.9.4-Perl-5.24.1<br>1.7.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded<br>1.7.2-IGB-gcc-8.2.0-Perl-5.28.1
−
|BioPerl project is an international association of developers of open source Perl tools for bioinformatics, genomics and life science research.
+
|Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
 
|-
 
|-
−
|[https://code.google.com/p/biopieces/ biopieces]
+
|[https://github.com/maasha/biopieces Biopieces]
−
|0.48
+
|2.0-IGB-gcc-4.9.4-Perl-5.24.1
−
|The Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks. The Biopieces work on a data stream in such a way that the data stream can be passed through several different Biopieces, each performing one specific task: modifying or adding records to the data stream, creating plots, or uploading data to databases and web services.
+
|Biopieces is a bioinformatic framework of tools easily used and easily created.
 
|-
 
|-
−
|[https://github.com/blahah/biopsy biopsy]
+
|[http://www.biopython.org Biopython]
−
|0.3.0
+
|1.68-IGB-gcc-4.9.4-Python-2.7.13<br>1.68-IGB-gcc-4.9.4-Python-3.6.1<br>1.76-IGB-gcc-4.9.4-Python-3.6.1<br>1.76-IGB-gcc-8.2.0-Python-3.7.2<br>1.79-IGB-gcc-8.2.0-Python-3.7.2<br>1.83-IGB-gcc-8.2.0-Python-3.10.1
−
|Biopsy is a framework for optimising the settings of any program or pipeline which produces a measurable output. It is particularly intended for bioinformatics, where computational pipelines take a long time to run, making optimisation of parameters using crude methods unfeasible. Biopsy will use a range of discrete optimisation strategies to rapidly find the settings that perform the best.
+
|Biopython is a set of freely available tools for biological computation writtenin Python by an international team of developers. It is a distributed collaborative effort todevelop Python libraries and applications which address the needs of current and future work inbioinformatics.  
 
|-
 
|-
−
|[http://www.bioinformatics.babraham.ac.uk/projects/bismark/ bismark]
+
|[https://github.com/cokelaer/bioservices bioservices]
−
|0.13.0, 0.14.5, 0.15.0, 0.16.1
+
|1.7.9-IGB-gcc-4.9.4-Python-3.6.1
−
|A bisulfite read mapper and methylation caller
+
|Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).
 
|-
 
|-
−
|[http://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastDocs&DOC_TYPE=Download blast+]
+
|[http://www.bioinformatics.babraham.ac.uk/projects/bismark/ Bismark]
−
|2.2.25+, 2.2.28+, 2.2.31, 2.3.0, 2.5.0, 2.6.0
+
|0.17.0-IGB-gcc-4.9.4-Perl-5.24.1<br>0.18.1-IGB-gcc-4.9.4-Perl-5.24.1<br>0.22.1-IGB-gcc-4.9.4-Perl-5.24.1<br>0.22.3-IGB-gcc-8.2.0-Perl-5.28.1
−
|BLAST+ is a new suite of BLAST tools that utilizes the NCBI C++ Toolkit. The BLAST+ applications have a number of performance and feature improvements over the legacy BLAST applications.
+
|A tool to map bisulfite converted sequence reads and determine cytosine methylation states
 
|-
 
|-
−
|[http://blast.ncbi.nlm.nih.gov/Blast.cgi blast-intel]
+
|Bison
−
|2.2.26
+
|
−
|The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
+
|Bison is a general-purpose parser generator that converts an annotated context-free grammarinto a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
 
|-
 
|-
−
|[http://blast.ncbi.nlm.nih.gov/Blast.cgi blast]
+
|[https://github.com/PacificBiosciences/blasr BLASR]
−
|2.2.26
+
|4.0.0-IGB-gcc-4.9.4
−
|The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
+
|BLASR (Basic Local Alignment with Successive Refinement) rapidly maps  reads to genomes by finding the highest scoring local alignment or set of local alignments  between the read and the genome. Optimized for PacBios extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.  
 
|-
 
|-
−
|[https://www.blast2go.com/ blast2go]
+
|[http://blast.ncbi.nlm.nih.gov/ BLAST]
−
|2.5
+
|2.2.26-Linux_x86_64
−
|Blast2GO is an ALL in ONE tool for functional annotation of (novel) sequences and the analysis of annotation data.
+
|Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
 
|-
 
|-
−
|[https://genome.ucsc.edu/FAQ/FAQblat.html blat]
+
|[http://blast.ncbi.nlm.nih.gov/ BLAST+]
−
|0.34
+
|2.10.1-IGB-gcc-8.2.0<br>2.13.0-IGB-gcc-8.2.0<br>2.2.31-IGB-gcc-4.9.4<br>2.6.0-IGB-gcc-4.9.4<br>2.7.1-IGB-gcc-4.9.4<br>2.9.0-IGB-gcc-4.9.4
−
|Blat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory.
+
|Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
 +
|-
 +
|[http://genome.ucsc.edu/FAQ/FAQblat.html BLAT]
 +
|3.5-IGB-gcc-4.9.4
 +
|BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
 
|-
 
|-
 
|[https://github.com/DRL/blobtools blobtools]
 
|[https://github.com/DRL/blobtools blobtools]
−
|0.9.19.5
+
|0.9.19.6-IGB-gcc-4.9.4-Python-2.7.13<br>1.0.1-IGB-gcc-4.9.4-Python-2.7.13<br>1.1.1-IGB-gcc-4.9.4-Python-3.6.1
−
|Application for the visualisation of (draft) genome assemblies and general assembly QC using TAGC (Taxon-annotated Gc-Coverage) plots
+
|Application for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots
 
|-
 
|-
−
|[http://www.boost.org/ boost-intel]
+
|[https://github.com/blobtoolkit/blobtools2/archive/refs/tags blobtools2]
−
|1.54
+
|2.6.1-IGB-gcc-4.9.4-Python-3.6.1<br>2.6.4-IGB-gcc-8.2.0-Python-3.7.2
 +
|Application for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots
 +
|-
 +
|[https://github.com/npm/cli bnpm]
 +
|v7.20.0-IGB-gcc-4.9.4
 +
|the package manager for JavaScript
 +
|-
 +
|Boost
 +
|
 
|Boost provides free peer-reviewed portable C++ source libraries.
 
|Boost provides free peer-reviewed portable C++ source libraries.
 
|-
 
|-
−
|[http://www.boost.org/ boost]
+
|Boost.Python
−
|1.54, 1.55, 1.59.0
+
|
 
|Boost provides free peer-reviewed portable C++ source libraries.
 
|Boost provides free peer-reviewed portable C++ source libraries.
 
|-
 
|-
−
|[http://bowtie-bio.sourceforge.net/index.shtml bowtie]
+
|[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
−
|0.12.8, 0.12.9, 1.0.0, 1.1.2
+
|1.1.2-IGB-gcc-4.9.4<br>1.2.0-IGB-gcc-4.9.4<br>1.2.2-IGB-gcc-4.9.4<br>1.3.0-IGB-gcc-8.2.0
−
|Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
+
|Bowtie is an ultrafast, memory-efficient short read aligner.It aligns short DNA sequences (reads) to the human genome.
 +
|-
 +
|[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]
 +
|2.1.0-IGB-gcc-4.9.4<br>2.3.1-IGB-gcc-4.9.4<br>2.3.2-IGB-gcc-4.9.4<br>2.3.5.1-IGB-gcc-4.9.4<br>2.4.1-IGB-gcc-8.2.0<br>2.4.2-IGB-gcc-8.2.0<br>2.4.5-IGB-gcc-8.2.0<br>2.5.3-IGB-gcc-8.2.0
 +
|Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads  to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s  of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome,  its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
 +
|-
 +
|[https://github.com/jenniferlu717/Bracken Bracken]
 +
|2.6.2-IGB-gcc-4.9.4<br>2.6.2-IGB-gcc-8.2.0
 +
|Bracken is a companion program to Kraken 1 or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample).
 
|-
 
|-
−
|[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml bowtie2]
+
|[https://github.com/Gaius-Augustus/BRAKER BRAKER]
−
|2.0.0-beta6, 2.0.2, 2.0.5, 2.1.0, 2.2.5, 2.2.6
+
|2.1.2-IGB-gcc-4.9.4<br>2.1.5-IGB-gcc-4.9.4<br>2.1.5-IGB-gcc-8.2.0<br>2.1.6-IGB-gcc-8.2.0<br>3.0.3-IGB-gcc-8.2.0
−
|Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
+
|BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
 
|-
 
|-
−
|[http://exon.gatech.edu/genemark/braker1.html BRAKER1]
+
|[http://bioinform.github.io/breakseq2/ BreakSeq2]
−
|1.9
+
|2.2-IGB-gcc-4.9.4-Python-2.7.13
−
|BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS
+
|Ultrafast and accurate nucleotide-resolution analysis of structural variants - Homepage: http://bioinform.github.io/breakseq2/
 
|-
 
|-
−
|[http://breakdancer.sourceforge.net/index.html breakdancer]
+
|[https://github.com/barricklab/breseq breseq]
−
|1.1
+
|0.31.0-IGB-gcc-4.9.4<br>0.36.1-IGB-gcc-8.2.0<br>0.37.0-IGB-gcc-8.2.0
−
|BreakDancer-1.1, released under GPLv3, is a Perl/Cpp package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
+
|is a computational pipeline for the analysis of short-read re-sequencing data (e.g. Illumina, 454, IonTorrent, etc.). It uses reference-based alignment approaches to predict mutations in a sample relative to an already sequenced genome.
 
|-
 
|-
−
|[http://barricklab.org/twiki/bin/view/Lab/ToolsBacterialGenomeResequencing breseq]
+
|[http://brig.sourceforge.net/ BRIG]
−
|0.24, 0.25d, 0.28.1
+
|0.95-Java-1.8.0_152
−
|breseq is a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. breseq is a command line tool implemented in C++ and R.
+
|BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
 
|-
 
|-
−
|[http://sourceforge.net/projects/rnaseqassembly/ bridger]
+
|[https://github.com/BSSeeker/BSseeker2 BS-Seeker]
−
|r2014-12-01
+
|2.1.2-IGB-gcc-4.9.4-Python-2.7.13
−
|Bridger is an efficient de novo transcriptome assembler for RNA-Seq data. It expects as input RNA-Seq reads (single or paired) in fasta or fastq format, outputs all transcripts in fasta format, without using a reference genome.
+
|BS Seeker 2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated short reads.
 
|-
 
|-
−
|[http://pellegrini.mcdb.ucla.edu/BS_Seeker2/ bs-seeker2]
+
|[https://github.com/hellbelly/BS-Snper BS-Snper]
−
|may-28-2014
+
|20170222-IGB-gcc-4.9.4-Perl-5.24.1
−
|A versatile aligning pipeline for bisulfite sequencing data
+
|BS-SNPer is an ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM/SAM format using approximate Bayesian modeling.
 
|-
 
|-
−
|[http://busco.ezlab.org/ busco]
+
|[http://busco.ezlab.org/ BUSCO]
−
|2.0, 3.0
+
|3.0.1-IGB-gcc-4.9.4-Python-2.7.13<br>4.1.4-IGB-gcc-8.2.0-Python-3.7.2<br>5.1.2-IGB-gcc-8.2.0-Python-3.7.2<br>5.3.2-IGB-gcc-8.2.0-Python-3.7.2<br>5.4.4-IGB-gcc-8.2.0-Python-3.7.2<br>5.5.0-IGB-gcc-8.2.0-Python-3.7.2
−
|BUSCO v3 provides quantitative measures for the assessment of genome assembly, gene set, and transcriptome completeness, based on evolutionarily-informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB v9.
+
|Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)
 
|-
 
|-
−
|[http://bio-bwa.sourceforge.net bwa]
+
|[http://bio-bwa.sourceforge.net/ BWA]
−
|0.5.9, 0.7.5a, 0.7.10, 0.7.15
+
|0.5.9-IGB-gcc-4.9.4<br>0.6.2-IGB-gcc-4.9.4<br>0.7.15-IGB-gcc-4.9.4<br>0.7.17-IGB-gcc-4.9.4<br>0.7.17-IGB-gcc-8.2.0
−
|BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome
+
|Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
 
|-
 
|-
−
|[https://github.com/BrendelGroup/BWASP BWASP]
+
|[https://github.com/bxlab/bx-python bx-python]
−
|20160106
+
|0.8.13-IGB-gcc-8.2.0-Python-3.7.2
−
|Bisulfite-seq data Workflow Automation Software and Protocols. The BWASP repository encompasses code we developed in the Brendel Group for scalable, reproducible analyses of bisulfite sequencing data.
+
|The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses.  
 +
|-
 +
|[http://invisible-island.net/byacc/byacc.html byacc]
 +
|20170709-IGB-gcc-4.9.4
 +
|Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available.In contrast to bison, it is written to avoid dependencies upon a particular compiler.
 
|-
 
|-
 
|[http://www.bzip.org/ bzip2]
 
|[http://www.bzip.org/ bzip2]
−
|1.0.6
+
|1.0.6-IGB-gcc-4.9.4<br>1.0.6-IGB-gcc-8.2.0
−
|bzip2 is a freely available, patent free (see below), high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
+
|bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
 +
|-
 +
|c-ares
 +
|
 +
|c-ares is a C library for asynchronous DNS requests (including name resolves)
 +
|-
 +
|[https://github.com/ComparativeGenomicsToolkit/cactus cactus]
 +
|20180705-IGB-gcc-4.9.4-Python-2.7.13
 +
|Cactus is a reference-free whole-genome multiple alignment program.
 +
|-
 +
|cairo
 +
|
 +
|Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
 
|-
 
|-
−
|[http://sites.bio.indiana.edu/~hahnlab/Software.html cafe]
+
|[https://github.com/marbl/canu Canu]
−
|2.2, 3.0
+
|1.4-IGB-gcc-4.9.4-Perl-5.24.1<br>1.5-IGB-gcc-4.9.4-Perl-5.24.1<br>1.6-IGB-gcc-4.9.4-Perl-5.24.1<br>1.7-IGB-gcc-4.9.4-Perl-5.24.1<br>1.7.1-IGB-gcc-4.9.4-Perl-5.24.1<br>1.8-IGB-gcc-4.9.4-Perl-5.24.1<br>1.9-IGB-gcc-8.2.0-Perl-5.28.1<br>2.0-IGB-gcc-8.2.0-Perl-5.28.1<br>2.1.1-IGB-gcc-8.2.0-Perl-5.28.1<br>2.2-IGB-gcc-8.2.0-Perl-5.28.1
−
|Computational analysis of (gene) family evolution.
+
|Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION).
 +
|-
 +
|[http://bioinformaticstools.mayo.edu/research/cap-mirseq/ cap-mirseq]
 +
|20200817-IGB-gcc-4.9.4
 +
|CAP-miRSeq: A comprehensive analysis pipeline for deep microRNA sequencing
 +
|-
 +
|capnproto
 +
|
 +
|Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. Think JSON, except binary. Or think Protocol Buffers, except faster.
 
|-
 
|-
−
|[https://github.com/marbl/canu canu]
+
|[https://github.com/IGBIllinois/cbc_pacbio cbc_pacbio]
−
|1.2, 1.3, 1.4, 1.5
+
|beta-IGB-gcc-8.2.0
−
|Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing (such as the PacBio RSII or Oxford Nanopore MinION). The software is currently alpha level, feel free to use and report issues encountered.
+
|Command-line scripts and pipelines to perform downstream analyses of Sequel II subreads
 
|-
 
|-
−
|[http://support.illumina.com/sequencing/sequencing_software/casava.html casava]
+
|[https://github.com/soedinglab/CCMpred CCMpred]
−
|1.8.2
+
|20191102-IGB-gcc-4.9.4
−
|The CASAVA 1.8.2 package processes sequencing reads provided by RTA or OLB.
+
|CCMpred is a C implementation of a Markov Random Field pseudo-likelihood maximization for learning protein residue-residue contacts as made popular by Ekeberg et al. [1] and Balakrishnan and Kamisetty [2].
 
|-
 
|-
−
|[http://ccl.cse.nd.edu/software/ cctools]
+
|[http://weizhong-lab.ucsd.edu/cd-hit/ CD-HIT]
−
|5.2.0
+
|4.6.6-IGB-gcc-4.9.4<br>4.8.1-IGB-gcc-8.2.0
−
|The Cooperative Computing Tools (cctools) contains Parrot, Chirp, Makeflow, Work Queue, SAND, and other software.
+
|CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
 
|-
 
|-
−
|[http://weizhong-lab.ucsd.edu/cd-hit/ cd-hit]
+
|[https://github.com/gpertea/cdbfasta cdbfasta]
−
|4.5.8, 4.6, 4.6.1, 4.6.1a
+
|20170316-IGB-gcc-4.9.4<br>20181005-IGB-gcc-8.2.0
−
|CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik's Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)
+
|CDB (Constant DataBase) indexing and retrieval tools for FASTA files
 
|-
 
|-
−
|[http://cdbfasta.sourceforge.net/ cdbfasta]
+
|[https://github.com/jrwnter/cddd cddd]
−
|0.99
+
|20200130-IGB-gcc-4.9.4-Python-3.6.1
−
|fast indexing and retrieval of fasta records from flat file databases.
+
|Continuous and Data-Driven Descriptors
 
|-
 
|-
−
|[http://korflab.ucdavis.edu/datasets/cegma/ cegma]
+
|[https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger cellranger]
−
|v2.4.010312
+
|2.1.0<br>2.1.1<br>3.0.0<br>3.0.1<br>3.1.0<br>4.0.0<br>5.0.0<br>6.0.1<br>6.0.2<br>6.1.1<br>7.0.0<br>7.0.1<br>7.1.0<br>7.2.0<br>8.0.0
−
|a computational method, CEGMA (Core Eukaryotic Genes Mapping Approach), for building a highly reliable set of gene annotations in the absence of experimental data.
+
|Cell Ranger is a set of analysis pipelines that process Chromium single cell 3 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
 
|-
 
|-
−
|[http://www.cgal.org/ cgal]
+
|[https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/what-is-cell-ranger-arc cellranger-arc]
−
|4.4
+
|1.0.0<br>2.0.1<br>2.0.2
−
|CGAL is a software project that provides easy access to efficient and reliable geometric algorithms in the form of a C++ library. CGAL is used in various areas needing geometric computation, such as geographic information systems, computer aided design, molecular biology, medical imaging, computer graphics, and robotics. The library offers data structures and algorithms like triangulations, Voronoi diagrams, Boolean operations on polygons and polyhedra, point set processing, arrangements of curves, surface and volume mesh generation, geometry processing, alpha shapes, convex hull algorithms, shape analysis, AABB and KD trees...
+
|Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage.
 
|-
 
|-
−
|[http://www.cgat.org/cgat/Tools/the-cgat-code-collection cgat]
+
|[https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac cellranger-atac]
−
|0.2.3
+
|1.1.0<br>1.2.0<br>2.0.0<br>2.1.0
−
|The CGAT code collection contains scripts and pipelines developed by CGAT. The collection contains scripts for genomics and next-generation sequencing analysis, but also general purpose scripts.
+
|Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.  
 
|-
 
|-
−
|[https://bitbucket.org/biobakery/cgfp cgfp]
+
|[https://ccb.jhu.edu/software/centrifuge/ centrifuge]
−
|20161205
+
|1.0.3-beta-IGB-gcc-4.9.4<br>1.0.4-beta-IGB-gcc-4.9.4
−
|This repository contains a protocol and several scripts to assist users in combining Sequence Similarity Network (SSN) information with ShortBRED output. This approach, called 'chemically-guided functional profiling,' is useful for studying large protein families in metagenomic and metatranscriptomic datasets.
+
|Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems.
 
|-
 
|-
−
|[http://song.igb.illinois.edu/chance.html chance]
+
|[https://ceres-solver.googlesource.com/ceres-solver ceres-solver]
−
|1.0
+
|1.14.0-IGB-gcc-4.9.4<br>1.14.0-IGB-gcc-8.2.0<br>2.0.0-IGB-gcc-8.2.0
−
|CHANCE - CHip-seq ANalytics and Confidence Estimation.
+
|Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems.
 
|-
 
|-
−
|[https://github.com/Ecogenomics/CheckM/wiki CheckM]
+
|[http://ecogenomics.github.io/CheckM CheckM]
−
|0.9.7
+
|1.0.7-IGB-gcc-4.9.4-Python-2.7.13<br>1.1.3-IGB-gcc-8.2.0-Python-3.7.2<br>1.1.9-IGB-gcc-8.2.0-Python-3.7.2
 
|CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
 
|CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
 
|-
 
|-
−
|[https://github.com/GuipengLi/ChIA-PET2 ChIA-PET2]
+
|[https://github.com/chklovski/CheckM2 CheckM2]
−
|0.9.2.1
+
|1.0.1
−
|ChIA-PET2 is a versatile and flexible pipeline for analysing different variants of ChIA-PET data from raw sequencing reads to chromatin loops.
+
|Unlike CheckM1, CheckM2 has universally trained machine learning models it applies regardless of taxonomic lineage to predict the completeness and contamination of genomic bins.
 +
|-
 +
|[https://bitbucket.org/valenlab/chopchop chopchop]
 +
|20190211-IGB-gcc-4.9.4-Python-2.7.13
 +
|CHOPCHOP is a python script that allows quick and customizable design of guide RNA. We support selecting target sites for CRISPR/Cas9, CRISPR/Cpf1 or TALEN with wide range of customization. We even support C2c2 for isoform targeting.
 +
|-
 +
|[https://catchenlab.life.illinois.edu/chromonomer/ Chromonomer]
 +
|1.13-IGB-gcc-8.2.0
 +
|Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.
 +
|-
 +
|[http://sanger-pathogens.github.io/circlator/ Circlator]
 +
|1.5.1-IGB-gcc-4.9.4-Python-3.6.1<br>1.5.5-IGB-gcc-8.2.0-Python-3.7.2
 +
|A tool to circularize genome assemblies.  
 
|-
 
|-
−
|[http://www.cgl.ucsf.edu/chimera/ chimera]
+
|[http://www.circos.ca/ Circos]
−
|1.5.3, 1.6.2
+
|0.69-4-IGB-gcc-4.9.4-Perl-5.24.1<br>0.69-9-IGB-gcc-8.2.0-Perl-5.28.1
−
|UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and animations can be generated.
+
|Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
 
|-
 
|-
−
|[http://www.cbs.dtu.dk/services/ChloroP/ chlorop]
+
|[http://www.biostat.jhsph.edu/~hji/cisgenome/ cisgenome]
−
|1.1
+
|2.0-IGB-gcc-4.9.4
−
|predicts the presence of chloroplast transit peptides (cTP) in protein sequences and the location of potential cTP cleavage sites.
+
|An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
 
|-
 
|-
−
|[http://compbio.mit.edu/ChromHMM/ ChromHMM]
+
|[https://pypi.org/project/clang-format clang-format]
−
|1.10
+
|15.0.7-IGB-gcc-8.2.0-Python-3.7.2
−
|ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. ChromHMM is based on a multivariate Hidden Markov Model that explicitly models the presence or absence of each chromatin mark. The resulting model can then be used to systematically annotate a genome in one or more cell types. By automatically computing state enrichments for large-scale functional and annotation datasets ChromHMM facilitates the biological characterization of each state. ChromHMM also produces files with genome-wide maps of chromatin state annotations that can be directly visualized in a genome browser.
+
|Clang-Format is an LLVM-based code formatting tool
 
|-
 
|-
−
|[http://sanger-pathogens.github.io/circlator/ circlator]
+
|[http://ccb.jhu.edu/people/florea/research/CLASS2/ CLASS2]
−
|1.4.1
+
|2.1.7-IGB-gcc-8.2.0
−
|A tool to circularize genome assemblies.
+
|CLASS2 is a fast and accurate program for transcript assembly of RNA-seq reads aligned to a reference genome. CLASS2 uses the splice graph model to represent a gene and its splice variants, and a dynamic programming optimization algorithm to score and select a subset of transcripts most likely present in the sample.  
 
|-
 
|-
−
|[http://jonathancrabtree.github.io/Circleator/index.html Circleator]
+
|[https://github.com/gamcil/clinker clinker]
−
|1.0.0rc4
+
|0.0.27-IGB-gcc-8.2.0-Python-3.7.2
−
|The Charm City Circleator–or Circleator for short–is a Perl-based visualization tool developed at the Institute for Genome Sciences in the University of Maryland’s School of Medicine.
+
|clinker is a pipeline for easily generating publication-quality gene cluster comparison figures.
 
|-
 
|-
−
|[http://circos.ca/software/download/circos/ circos]
+
|[https://github.com/YeoLab/clipper clipper]
−
|0.67
+
|1.2.1-IGB-gcc-4.9.4-Python-2.7.13
−
|Circos is a software package for visualizing data and information. It visualizes data in a circular layout . this makes Circos ideal for exploring relationships between objects or positions. There are other reasons why a circular layout is advantageous, not the least being the fact that it is attractive.
+
|A tool to detect CLIP-seq peaks.
 
|-
 
|-
−
|[http://sb.nhri.org.tw/CISA/en/CISA cisa]
+
|Clp
−
|1.3
+
|
−
|CISA: Contig Integrator for Sequence Assembly
+
|Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.
 
|-
 
|-
−
|[http://www.biostat.jhsph.edu/~hji/cisgenome/ cisgenome]
+
|[https://rosenberglab.stanford.edu/clumpp.html CLUMPP]
−
|2.0
+
|1.1.2
−
|An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
+
|CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses.
 
|-
 
|-
−
|[http://veda.cs.uiuc.edu/cisMetalysis/ cisMetalysis]
+
|[http://www.clustal.org/omega/ Clustal-Omega]
−
|1.3
+
|1.2.4-IGB-gcc-4.9.4<br>1.2.4-IGB-gcc-8.2.0
−
|New meta-analysis tools reveal common transcriptional regulatory basis for multiple determinants of behavior
+
|Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms
 
|-
 
|-
−
|[http://www.xavierdidelot.xtreemhost.com/clonalframe.htm ClonalFrame]
+
|[http://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2]
−
|1.2
+
|2.1-IGB-gcc-4.9.4
−
|in a nutshell, ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.
+
|ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. - Homepage: http://www.ebi.ac.uk/Tools/msa/clustalw2/
 
|-
 
|-
−
|[http://www.clustal.org/omega/ clustal-omega]
+
|[http://clusterflow.io/ clusterflow]
−
|1.2.1
+
|0.5-IGB-gcc-4.9.4-Perl-5.24.1
−
|Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours.
+
|Cluster Flow is workflow manager designed to run bioinformatics pipelines. It is operated through a single command cf, which can be used to launch, configure, monitor and cancel pipelines.
 
|-
 
|-
−
|[http://www.clustal.org/clustal2/ clustalw]
+
|CMake
−
|2.1
+
|
−
|Clustal W is a general purpose multiple alignment program for DNA or proteins.
+
|CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
 
|-
 
|-
−
|[http://www.cmake.org/cmake/resources/software.html cmake]
+
|[https://github.com/etal/cnvkit CNVkit]
−
|2.8.12.2, 3.3.1, 3.8.0
+
|0.9.10-IGB-gcc-8.2.0-Python-3.10.1<br>0.9.8-IGB-gcc-8.2.0-Python-3.7.2
−
|CMake, the cross-platform, open-source build system
+
|A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
 
|-
 
|-
−
|[https://github.com/abyzovlab/CNVnator cnvnator]
+
|[https://github.com/abyzovlab/CNVnator CNVnator]
−
|0.3.2
+
|0.3.3-IGB-gcc-4.9.4<br>0.3.3-IGB-gcc-4.9.4-Python-2.7.13
 
|a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
 
|a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
 +
|-
 +
|[https://github.com/cocodataset/cocoapi cocoapi]
 +
|20190218-IGB-gcc-4.9.4-Python-3.6.1
 +
|OCO is a large image dataset designed for object detection, segmentation, person keypoints detection, stuff segmentation, and caption generation.
 +
|-
 +
|[https://github.com/colmap/colmap/tree/dev colmap]
 +
|20210330-IGB-gcc-4.9.4
 +
|COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface. It offers a wide range of features for reconstruction of ordered and unordered image collections.
 
|-
 
|-
 
|[https://github.com/BinPro/CONCOCT CONCOCT]
 
|[https://github.com/BinPro/CONCOCT CONCOCT]
−
|0.4.1
+
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1<br>1.1.0-IGB-gcc-8.2.0-Python-3.7.2
 
|A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
 
|A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
 +
|-
 +
|[https://github.com/open2c/cooler cooler]
 +
|0.8.11-IGB-gcc-8.2.0-Python-3.7.2<br>0.8.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
 +
|-
 +
|[https://github.com/open2c/cooltools cooltools]
 +
|0.4.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|The tools for your .cools
 +
|-
 +
|[https://github.com/Zhao-Group/COPIES COPIES]
 +
|20231202-IGB-gcc-8.2.0-Python-3.10.1
 +
|COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites (CRISPR-COPIES) is a user-friendly web application and a command line tool for rapid discovery of neutral integration sites.
 
|-
 
|-
 
|[http://www.gnu.org/software/coreutils/coreutils.html coreutils]
 
|[http://www.gnu.org/software/coreutils/coreutils.html coreutils]
−
|8.27
+
|8.28-IGB-gcc-4.9.4<br>8.28-IGB-gcc-8.2.0<br>9.1-IGB-gcc-8.2.0
−
|The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.
+
|The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system.These are the core utilities which are expected to exist on every operating system.
 +
|-
 +
|[https://github.com/iqbal-lab/cortex cortex]
 +
|1.0.5.21-IGB-gcc-4.9.4
 +
|reference free variant assembly
 +
|-
 +
|CppUnit
 +
|
 +
|CppUnit is the C++ port of the famous JUnit framework for unit testing.
 +
|-
 +
|[https://github.com/cboursnell/crb-blast crb-blast]
 +
|0.6.9-IGB-gcc-4.9.4
 +
|Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
 
|-
 
|-
−
|[http://bioinformatics.ninja/crass/ crass]
+
|[https://www.animalgenome.org/tools/share/crimap/ crimap]
−
|0.3.12
+
|2.507-IGB-gcc-8.2.0
−
|Crass was designed primarily for short read data like the kind produced from the Illumina sequencing platform. However it has been tested on Sanger and Ion Torrent data as well. The current constraints are that reads shorter than 76bp in length will not be used and reads longer than 2000bp cannot be used
+
|CRI-MAP (version 2.4, by Phil Green et al, 1990) has been used extensively in the past 20 years for genetic linkage analysis of diploid species, and has played a fundamental role in producing genetic linkage maps for humans, rats, mouse, fruit flies, cattle, sheep, pigs, chicken, fish, among many other species.  
 
|-
 
|-
−
|[http://bioinformatics.ninja/crisprtools/ crisprtools]
+
|[https://github.com/broadinstitute/cromwell cromwell]
−
|0.1.8
+
|39-Java-1.8.0_152
−
|Crisprtools was developed to parse the crispr file format, which is an xml markup for describing Clustered Regularly Interspersed Short Palindromic Repeats. Crisprtools is written in c++ and uses libcrispr for all the heavy lifting.
+
|Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
 
|-
 
|-
−
|[http://www.nvidia.com/object/cuda_home_new.html cuda]
+
|[https://crossmap.sourceforge.net/ Crossmap]
−
|8.0
+
|0.6.5-IGB-gcc-8.2.0-Python-3.7.2
−
|CUDA® is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). - See more at: http://www.nvidia.com/object/cuda_home_new.html#sthash.zHTOOaHX.dpuf
+
|CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.
 
|-
 
|-
−
|[http://cufflinks.cbcb.umd.edu/ cufflinks]
+
|[https://developer.nvidia.com/cuda-toolkit CUDA]
−
|1.1.0, 1.3.0, 2.0.2, 2.1.1, 2.2.0, 2.2.1
+
|10.0.130<br>10.1.105<br>11.0.3<br>11.1.0<br>11.2.2<br>11.3.0<br>11.8.0<br>8.0.61<br>8.0.61-IGB-gcc-4.9.4<br>9.0.176<br>9.1.85
−
|Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. It accepts aligned RNA-Seq reads and assembles the alignments into a parsimonious set of transcripts. Cufflinks then estimates the relative abundances of these transcripts based on how many reads support each one, taking into account biases in library preparation protocols.
+
|CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
 
|-
 
|-
−
|[https://curl.haxx.se/libcurl/ curl]
+
|[https://developer.nvidia.com/cudnn cuDNN]
−
|7.49.1
+
|5.1-CUDA-8.0.61<br>5.1-IGB-gcc-4.9.4-CUDA-8.0.61<br>6.0-IGB-gcc-4.9.4-CUDA-8.0.61<br>7.0.5-CUDA-9.0.176<br>7.1.4-CUDA-9.0.176<br>7.6.1.34-CUDA-10.0.130<br>8.0.4.30-CUDA-10.1.105<br>8.0.4.30-CUDA-11.1.0<br>8.1.1.33-CUDA-11.2.2<br>8.2.1.32-CUDA-11.3.0<br>8.9.2.23-CUDA-11.8.0
−
|libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP.
+
|The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for    deep neural networks.
 
|-
 
|-
−
|[https://code.google.com/p/cutadapt/ cutadapt]
+
|[http://cole-trapnell-lab.github.io/cufflinks/ Cufflinks]
−
|1.8.1
+
|2.2.1<br>2.2.1-IGB-gcc-4.9.4-b4fa050
−
|cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced for example when sequencing microRNAs.
+
|Transcript assembly, differential expression, and differential regulation for RNA-Seq
 
|-
 
|-
−
|[http://cython.org/ cython]
+
|[http://cunit.sourceforge.net/ CUnit]
−
|0.21.1
+
|2.1-3-IGB-gcc-4.9.4
−
|Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
+
|CUnit is a lightweight system for writing, administering, and running unit tests in C. It provides C programmers a basic testing functionality with a flexible variety of user interfaces.
 
|-
 
|-
−
|[http://www.cytoscape.org/ cytoscape]
+
|cURL
−
|2.8.1, 2.8.3
+
|
−
|Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data. A lot of Apps are available for various kinds of problem domains, including bioinformatics, social network analysis, and semantic web.
+
|libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
 
|-
 
|-
−
|[https://github.com/thegenemyers/DALIGNER DALIGNER]
+
|[http://opensource.scilifelab.se/projects/cutadapt/ cutadapt]
−
|20150421
+
|1.14-IGB-gcc-4.9.4-Python-2.7.13<br>1.17-IGB-gcc-4.9.4-Python-3.6.1<br>2.10-IGB-gcc-8.2.0-Python-3.7.2<br>3.7-IGB-gcc-8.2.0-Python-3.7.2
−
|The commands below permit one to find all significant local alignments between reads encoded in Dazzler database.
+
|Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.  
 
|-
 
|-
−
|[https://github.com/thegenemyers/DAZZ_DB DAZZ_DB]
+
|[https://github.com/tjiangHIT/cuteSV cuteSV]
−
|20150421
+
|1.0.12-IGB-gcc-8.2.0-Python-3.7.2
−
|To facilitate the multiple phases of the dazzler assembler, we organize all the read data into what is effectively a database of the reads and their meta-information.
+
|A sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.
 
|-
 
|-
−
|[http://deconseq.sourceforge.net/ deconseq]
+
|[https://cytoscape.org/ cytoscape]
−
|0.4.3
+
|3.7.0-Java-1.8.0_152<br>3.8.2-Java-11.0.5<br>3.9.1-Java-11.0.5
−
|The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
+
|Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
 +
|-
 +
|[http://owenjm.github.io/damidseq_pipeline/ damidseq]
 +
|1.4-IGB-gcc-4.9.4
 +
|Processing DamID-seq data involves extending single-end reads, aligning the reads to the genome and determining the coverage, similar to processing regular ChIP-seq datasets.
 +
|-
 +
|[https://github.com/KHanghoj/DamMet DamMet]
 +
|1.0.2-IGB-gcc-8.2.0
 +
|DamMet is probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.
 +
|-
 +
|[https://sites.google.com/site/danposdoc/news DANPOS]
 +
|2.2.2-IGB-gcc-4.9.4-Python-2.7.13-R-3.3.3
 +
|A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2
 +
|-
 +
|[https://github.com/cmks/DAS_Tool DAS_Tool]
 +
|1.1.2-IGB-gcc-4.9.4
 +
|DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
 +
|-
 +
|[http://www.oracle.com/technetwork/products/berkeleydb DB]
 +
|18.1.32-IGB-gcc-4.9.4
 +
|Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
 +
|-
 +
|[https://bitbucket.org/kaistsystemsbiology/deepec DeepEC]
 +
|20190806-IGB-gcc-4.9.4-Python-3.6.1
 +
|DeepEC
 +
|-
 +
|[http://www.mousemotorlab.org/deeplabcut deeplabcut]
 +
|2.1.8.2-IGB-gcc-4.9.4-Python-3.6.1<br>2.2.1.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|Markerless pose estimation of user-defined features with deep learning for all animals
 
|-
 
|-
 
|[https://github.com/fidelram/deepTools deepTools]
 
|[https://github.com/fidelram/deepTools deepTools]
−
|1.6.0, 2.0
+
|2.5.3-IGB-gcc-4.9.4-Python-2.7.13<br>3.0.1-IGB-gcc-4.9.4-Python-2.7.13<br>3.2.1-IGB-gcc-4.9.4-Python-3.6.1<br>3.5.2-IGB-gcc-4.9.4-Python-3.6.1<br>3.5.2-IGB-gcc-8.2.0-Python-3.7.2
−
|deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. To do so, deepTools contains useful modules to process the mapped reads data to create coverage files in standard bedGraph and bigWig file formats.
+
|deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
 
|-
 
|-
 
|[https://github.com/spragunr/deep_q_rl deep_q_rl]
 
|[https://github.com/spragunr/deep_q_rl deep_q_rl]
−
|20170324
+
|20160603-IGB-gcc-4.9.4-Python-2.7.13
−
|This package provides a Lasagne/Theano-based implementation of the deep Q-learning algorithm described in:
+
|This package provides a Lasagne/Theano-based implementation of the deep Q-learning algorithm described in:Playing Atari with Deep Reinforcement Learning Volodymyr Mnih, Koray Kavukcuoglu, David Silver, Alex Graves, Ioannis Antonoglou, Daan Wierstra, Martin RiedmillerandMnih, Volodymyr, et al. "Human-level control through deep reinforcement learning." Nature 518.7540 (2015): 529-533.
 +
|-
 +
|[https://github.com/dellytools/delly delly]
 +
|0.8.1-IGB-gcc-4.9.4
 +
|Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.
 +
|-
 +
|[https://dendropy.org/ DendroPy]
 +
|4.4.0-IGB-gcc-4.9.4-Python-3.6.1<br>4.4.0-IGB-gcc-8.2.0-Python-3.7.2
 +
|DendroPy is a Python library for phylogenetic computing.
 +
|-
 +
|[https://gitee.com/bxxu/denopa deNOPA]
 +
|1.0.2-IGB-gcc-4.9.4-Python-2.7.13
 +
|As the basal bricks, the dynamics and arrangement of nucleosomes orchestrate the higher architecture of chromatin in a fundamental way, thereby affecting almost all nuclear biology processes.
 +
|-
 +
|[https://github.com/facebookresearch/detectron2/ detectron2]
 +
|0.2.1-IGB-gcc-4.9.4-Python-3.6.1<br>0.2.1-IGB-gcc-8.2.0-Python-3.7.2<br>0.5-IGB-gcc-8.2.0-Python-3.7.2<br>0.6-IGB-gcc-8.2.0-Python-3.7.2
 +
|Detectron2 is Facebook AI Research's next generation software system that implements state-of-the-art object detection algorithms
 +
|-
 +
|[https://github.com/bbuchfink/diamond DIAMOND]
 +
|0.8.38-IGB-gcc-4.9.4<br>0.9.10-IGB-gcc-4.9.4<br>0.9.16-IGB-gcc-4.9.4<br>0.9.22-IGB-gcc-4.9.4<br>0.9.24-IGB-gcc-4.9.4<br>0.9.24-IGB-gcc-8.2.0<br>0.9.36-IGB-gcc-8.2.0<br>0.9.9-IGB-gcc-4.9.4<br>2.0.15-IGB-gcc-8.2.0<br>2.0.6-IGB-gcc-8.2.0<br>2.0.9-IGB-gcc-8.2.0
 +
|Accelerated BLAST compatible local sequence aligner
 +
|-
 +
|[https://github.com/shenlab-sinai/diffreps diffReps]
 +
|1.55.6-IGB-gcc-4.9.4-Perl-5.24.1
 +
|ChIP-seq is now widely used to profile the protein DNA interactions on a genome. It is of high interest to compare the differential enrichment of a histone mark or transcription factor between two contrasting conditions, such as disease vs. control. diffReps is developed to serve this purpose. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. - Homepage: https://github.com/shenlab-sinai/diffreps
 
|-
 
|-
−
|[https://pythonhosted.org/DendroPy/ dendropy]
+
|[http://www.broadinstitute.org/software/discovar/blog/ DISCOVARdenovo]
−
|3.12.0, 4.0.3
+
|52488-IGB-gcc-4.9.4
−
|DendroPy is a Python library for phylogenetic computing. It provides classes and functions for the simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in a range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA, etc. Application scripts for performing some useful phylogenetic operations, such as data conversion and tree posterior distribution summarization, are also distributed and installed as part of the libary. DendroPy can thus function as a stand-alone library for phylogenetics, a component of more complex multi-library phyloinformatic pipelines, or as a scripting .glue. that assembles and drives such pipelines.
+
|DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.
 
|-
 
|-
−
|[http://deweylab.biostat.wisc.edu/detonate/ detonate]
+
|[http://www.crypticlineage.net/pages/distruct.html distruct]
−
|1.9
+
|2.2-IGB-gcc-4.9.4
−
|DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences.
+
|Modified version of the original distruct.py
 
|-
 
|-
−
|[http://ab.inf.uni-tuebingen.de/software/diamond/ diamond]
+
|[http://www1.montpellier.inra.fr/CBGP/diyabc/index.php DIYABC]
−
|0.6.13, 0.7.9, 0.8.5, 0.8.36
+
|2.1.0
−
|DIAMOND is a new high-throughput program for aligning a file of short reads against a protein reference database such as NR, at 20,000 times the speed of BLASTX, with high sensitivity
+
|a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers
 
|-
 
|-
−
|[http://www.broadinstitute.org/software/discovar/blog/ DISCOVAR-denovo]
+
|[https://github.com/diyabc/diyabc diyabc]
−
|52488
+
|1.1.28
−
|DISCOVAR de novo can generate de novo assemblies for both large and small genomes.
+
|DIYABC RF V1.0
 
|-
 
|-
−
|[http://genome.sph.umich.edu/wiki/DosageConvertor DosageConvertor]
+
|[https://jbloomlab.github.io/dms_tools2/ dms-tools2]
−
|1.0.3
+
|2.6.10-IGB-gcc-8.2.0-Python-3.7.2
−
|DosageConvertor is a C++ tool to convert dosage files (in VCF format) from Minimac3 to ther formats such as MaCH or PLINK.
+
|dms_tools2 is a software package for analyzing deep mutational scanning data. It is tailored to analyze libraries created using comprehensive codon mutagenesis of protein-coding genes, and perform analyses that are common to the Bloom lab,
 +
|-
 +
|[https://github.com/nanoporetech/dorado dorado]
 +
|0.6.0
 +
|Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
 
|-
 
|-
−
|[http://bioinformatics.bc.edu/marthlab/wiki/index.php/EagleView EagleView]
+
|[http://www.doxygen.org Doxygen]
−
|2.2
+
|1.8.13-IGB-gcc-4.9.4
−
|EagleView is an information-rich genome assembler viewer with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation.
+
|Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
 
|-
 
|-
−
|[http://www.ncbi.nlm.nih.gov/books/NBK179288/ edirect]
+
|[https://drep.readthedocs.io/en/latest/ drep]
−
|20150409
+
|3.2.0-IGB-gcc-8.2.0-Python-3.7.2
−
|Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
+
|dRep is a python program which performs rapid pair-wise comparison of genome sets. One of it’s major purposes is for genome de-replication, but it can do a lot more.
 
|-
 
|-
−
|[http://sccn.ucsd.edu/eeglab/ eeglab]
+
|[https://github.com/SpectraLogic/ds3_java_cli/ ds3_java_cli]
−
|13.3.2b
+
|5.1.2<br>5.1.4
−
|EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.
+
|Command line utilities for Bioarchive
 
|-
 
|-
−
|efidb
+
|[http://expressionanalysis.github.io/ea-utils/ ea-utils]
−
|00000000, 20150212, 20150403, 20150522, 20150804, 20151013, 20151209, 20160219, 20160414, 20160609, 20160921, 20161121, 20170412, 20170515
+
|1.04.807-IGB-gcc-4.9.4
−
|Env variables for EFI database release 64
+
|Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
 
|-
 
|-
−
|efidb_v2
+
|[https://easybuilders.github.io/easybuild EasyBuild]
−
|ip62, ip63, ip64, urtest
+
|4.6.2
−
|Env variables for EFI database release 63
+
|EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
 
|-
 
|-
−
|efiest
+
|[https://github.com/Rostlab/EAT EAT]
−
|alpha, beta, devel
+
|1.0.0-IGB-gcc-8.2.0-Python-3.7.2
−
|adds environmental variables for EFI QUEST development branch
+
|Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer annotations from a set of labeled lookup protein embeddings to query protein embeddings.
 
|-
 
|-
−
|efiest_v2
+
|[https://www.ncbi.nlm.nih.gov/books/NBK179288/ EDirect]
−
|beta, cd-hit-local, devel, devlocal, prod, shared, sharedbeta, sharedlocal
+
|20160310-IGB-gcc-4.9.4
−
|adds environmental variables for EFI shared library development branch
+
|Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
 
|-
 
|-
−
|efignn
+
|[https://sccn.ucsd.edu/eeglab/index.php eeglab]
−
|0.0.0, 0.2.0, 0.2.1, 0.2.2, 0.2.4
+
|2021.1-IGB-gcc-8.2.0
−
|adds environmental variables for EFI QUEST development branch
+
|EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.
 
|-
 
|-
−
|efignn_v2
+
|[https://github.com/eggnogdb/eggnog-mapper eggnog-mapper]
−
|beta, devel, devlocal, prod
+
|2.1.12-IGB-gcc-8.2.0-Python-3.7.2
−
|adds environmental variables for EFI GNT prod branch
+
|EggNOG-mapper is a tool for fast functional annotation of novel sequences.
 
|-
 
|-
−
|[http://eigen.tuxfamily.org/ eigen]
+
|Eigen
−
|2.0.17, 3.2.4
+
|
 
|Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
 
|Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
 
|-
 
|-
−
|[http://www.gnu.org/software/emacs/ emacs]
+
|[https://github.com/DReichLab/EIG eigensoft]
−
|24.3
+
|7.2.1-IGB-gcc-4.9.4
−
|GNU Emacs is an extensible, customizable text editor—and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
+
|The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006).  
 
|-
 
|-
 
|[http://emboss.sourceforge.net/ EMBOSS]
 
|[http://emboss.sourceforge.net/ EMBOSS]
−
|6.5.7
+
|6.6.0-IGB-gcc-4.9.4-Java-1.8.0_121
−
|EMBOSS is The European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.
+
|EMBOSS, The European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
 +
|-
 +
|[https://github.com/csmiller/EMIRGE EMIRGE]
 +
|0.61.1-IGB-gcc-4.9.4-Python-2.7.13
 +
|EMIRGE reconstructs full length ribosomal genes from short readsequencing data.  In the process, it also provides estimates of thesequences abundances.
 +
|-
 +
|[https://github.com/Pbdas/epa-ng epa-ng]
 +
|0.3.8-IGB-gcc-8.2.0
 +
|EPA-ng is a complete rewrite of the Evolutionary Placement Algorithm (EPA), previously implemented in RAxML. It uses libpll and pll-modules to perform maximum likelihood-based phylogenetic placement of genetic sequences on a user-supplied reference tree and alignment.
 +
|-
 +
|[https://github.com/biocore-ntnu/epic epic]
 +
|0.2.9-IGB-gcc-4.9.4-Python-2.7.13
 +
|epic is a software package for finding medium to diffusely enriched domains in chip-seq data. It is a fast, parallel and memory-efficient implementation of the incredibly popular SICER algorithm.
 +
|-
 +
|[https://github.com/biocore-ntnu/epic2 epic2]
 +
|0.0.41-IGB-gcc-4.9.4-Python-3.6.1
 +
|epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use.
 +
|-
 +
|[https://evidencemodeler.github.io/ EVidenceModeler]
 +
|1.1.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded<br>1.1.1-IGB-gcc-8.2.0-Perl-5.28.1
 +
|The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.
 +
|-
 +
|[https://github.com/brianhie/evolocity evolocity]
 +
|0.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|Evolocity is a Python package that implements evolutionary velocity, which constructs landscapes of protein evolution by using the local evolutionary predictions enabled by language models to predict the directionality of evolution and is described in the paper "Evolutionary velocity with protein language models" by Brian Hie, Kevin Yang, and Peter Kim.
 
|-
 
|-
−
|[https://github.com/csmiller/EMIRGE emirge]
+
|[https://exiftool.org/ exiftool]
−
|july-21-2014
+
|12.54-IGB-gcc-8.2.0-Perl-5.28.1
−
|EMIRGE reconstructs full length ribosomal genes from short read sequencing data.
+
|Read, Write and Edit Meta Information!
 
|-
 
|-
−
|[http://woldlab.caltech.edu/rnaseq erange]
+
|[https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate exonerate]
−
|3.2.1, 3.3.0
+
|2.2.0-IGB-gcc-4.9.4<br>2.2.0-IGB-gcc-8.2.0
−
|A package of python scripts designed to analyze ultra-high-througphut sequencing data from the Illumina/Solexa platform for RNA-seq and ChIP-seq in metazoan genomes. The RNA-seq portion of ERANGE is described in our Nature Methods paper 'Mapping and quantifying mammalian transcriptomes by RNA-Seq' (Mortazavi, 2008). ERANGE is built on top of Cistematic.
+
|Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
 
|-
 
|-
−
|[http://erpinfo.org/erplab erplab]
+
|[https://gitlab.com/ExonOntology/ExonOntology ExonOntology]
−
|4.0.2.3
+
|20171018-IGB-gcc-8.2.0-Perl-5.28.1
−
|ERPLAB Toolbox is a free, open-source Matlab package for analyzing ERP data. It is tightly integrated with EEGLAB Toolbox, extending EEGLAB’s capabilities to provide robust, industrial-strength tools for ERP processing, visualization, and analysis. A graphical user interface makes it easy for beginners to learn, and Matlab scripting provides enormous power for intermediate and advanced users.
+
|This project consists of a set of scripts that are necessary to perform offline Exon Ontology analyses. Briefly, it can accept a list of genomic sequences as input that represent exons (or parts of exons). The algorithm then retrieves the protein features that are encoded by these DNA sequences.
 
|-
 
|-
−
|est-precompute
+
|expat
−
|0, 48, 49, 50, 51, 52
+
|
−
|Homepage:
+
|Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
 
|-
 
|-
−
|[http://estscan.sourceforge.net/ estscan]
+
|[https://github.com/facebookresearch/esm#available fair-esm]
−
|3.0.3
+
|0.4.0-IGB-gcc-8.2.0-Python-3.7.2<br>2.0.0-IGB-gcc-8.2.0-Python-3.7.2
−
|ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts.
+
|This repository contains code and pre-trained weights for Transformer protein language models from Facebook AI Research, including our state-of-the-art ESM-1b and MSA Transformer.
 
|-
 
|-
−
|[http://pythonhosted.org/ete2/ ete2]
+
|[http://pb-falcon.readthedocs.io/en/latest/index.html FALCON]
−
|2.2.1072
+
|1.8.8-IGB-gcc-4.9.4-Python-2.7.13
−
|ETE is a python programming toolkit that assists in the automated manipulation, analysis and visualization of phylogenetic trees. It provides a wide range of tree handling options, node annotation features, programmatic access to the phylomeDB database (containing thousands of pre-calculated phylogenetic trees), and automatic orthology and paralogy detection. In addition, ETE implements an interactive tree visualization system as well as a highly customizable tree drawing engine to create PDF and SVG tree images. Note that, although ETE is mainly developed as a tool for phylogenetic analysis, it can also be used to deal with clustering trees or any other data that can be represented as a hierarchical tree.
+
|FALCON is a diploid aware genome assembler designed for Pacific Biosciences long read data.
 
|-
 
|-
−
|[http://www.ebi.ac.uk/~guy/exonerate/ exonerate]
+
|[https://github.com/md5sam/Falcon2Fastg Falcon2Fastg]
−
|2.2.0
+
|0.3.1-IGB-gcc-4.9.4-Python-2.7.13
−
|exonerate is a generic tool for pairwise sequence comparison.
+
|This software converts the results of PacBio assembly using FALCON, to a FASTG graph that can be visualized using Bandage.
 
|-
 
|-
−
|[http://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml fasta]
+
|[https://github.com/PacificBiosciences/FALCON_unzip FALCON_unzip]
−
|36.3.5d
+
|0.4.0-IGB-gcc-4.9.4-Python-2.7.13
−
|The FASTA programs find regions of local or global similarity between Protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. Other programs provide information on the statistical significance of an alignment. Like BLAST, FASTA can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
+
|FALCON-Unzip contains the modules that works with FALCON for full diploid assembly (representing haplotype specific contigs as "haplotigs" as assembly output).
 
|-
 
|-
−
|[http://kirill-kryukov.com/study/tools/fasta-splitter/ fasta_splitter]
+
|[https://github.com/mateidavid/fast5 fast5]
−
|0.1.1
+
|0.6.2-IGB-gcc-4.9.4<br>0.6.3-IGB-gcc-4.9.4<br>0.6.5-IGB-gcc-4.9.4<br>0.6.5-IGB-gcc-8.2.0
−
|This script divides a large FASTA file into a set of smaller, approximately equally sized files. It works with whole sequences, never dividing a sequence in the middle.
+
|A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
 
|-
 
|-
−
|[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ fastqc]
+
|[https://fasta.bioch.virginia.edu/wrpearson/fasta/fasta2/ fasta2]
−
|0.10.1, 0.11.2, 0.11.4, 0.11.5
+
|21.1.1-IGB-gcc-8.2.0
−
|FastQC aims to provide a simple way to do some quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis.
+
|
 
|-
 
|-
−
|[http://cmpg.unibe.ch/software/fastsimcoal2/ fastsimcoal2]
+
|[https://github.com/ParBliSS/FastANI FastANI]
−
|1.1.1, 2.5.2.21
+
|1.32
−
|While preserving all the simulation flexibility of simcoal2, fastsimcoal is now implemented under a faster continous-time sequential Markovian coalescent approximation, allowing it to efficiently generate genetic diversity for different types of markers along large genomic regions, for both present or ancient samples. It includes a parameter sampler allowing its integration into Bayesian or likelihood parameter estimation procedure.
+
|FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes.  
 
|-
 
|-
−
|[http://www.microbesonline.org/fasttree/ fasttree]
+
|[http://www.atgc-montpellier.fr/fastme/binaries.php FastME]
−
|2.1.7
+
|2.1.6.1-IGB-gcc-4.9.4<br>2.1.6.3-IGB-gcc-8.2.0
−
|FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7
+
|FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of NJ. FastME improves over NJ by performing topological moves using fast, sophisticated algorithms.
 
|-
 
|-
−
|[http://sourceforge.net/projects/fastuniq/files/ fastuniq]
+
|[https://miso.readthedocs.io/en/fastmiso/index.html fastmiso]
−
|1.1
+
|0.5.4-IGB-gcc-4.9.4-Python-2.7.13
−
|FastUniq as an ultrafast de novo tool for removal of duplicates in paired short DNA sequence reads in FASTQ format. FastUniq identifies duplicates by comparing sequences between read pairs and does not require complete genome sequences as prerequisites. FastUniq is capable of simultaneously handling reads with different lengths and results in highly efficient running time.
+
|MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.  
 
|-
 
|-
−
|[http://hannonlab.cshl.edu/fastx_toolkit/ fastx_toolkit]
+
|[https://github.com/OpenGene/fastp fastp]
−
|0.0.13, 0.0.14
+
|0.19.5-IGB-gcc-4.9.4<br>0.19.6-IGB-gcc-4.9.4-7117eba<br>0.20.0-IGB-gcc-4.9.4<br>0.23.4
−
|The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
+
|A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
 
|-
 
|-
−
|fdupes
+
|[http://scheet.org/software.html fastPHASE]
−
|1.6.1
+
|20160330
−
|FDUPES is a program for identifying duplicate files residing
+
|astPHASE is a program to estimate missing genotypes and unobserved haplotypes.
 
|-
 
|-
−
|[http://www.ffmpeg.org/index.html ffmpeg]
+
|[https://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ FastQ-Screen]
−
|2.1.3
+
|0.14.1-IGB-gcc-8.2.0
−
|FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. It includes libavcodec - the leading audio/video codec library
+
|FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
 
|-
 
|-
−
|[http://www.fftw.org/download.html fftw]
+
|[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FastQC]
−
|3.3.5
+
|0.11.5-Java-1.8.0_201<br>0.11.8-Java-1.8.0_152<br>0.11.9-Java-1.8.0_201
−
|FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data (as well as of even/odd data, i.e. the discrete cosine/sine transforms or DCT/DST).
+
|FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
 
|-
 
|-
−
|[http://www.bcgsc.ca/platform/bioinfo/software/findpeaks findpeaks]
+
|[https://rajanil.github.io/fastStructure/ fastStructure]
−
|3.1.9.2
+
|1.0-IGB-gcc-4.9.4-Python-2.7.13
−
|Findpeaks was developed to perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest. A minimum height threshold is used to determine which 'peaks' are shown in the UCSC compatible wig file - if no threshold is use, all reads are shown. It collects and sorts the reads along each chromosomes, and identifies areas of enrichment, termed 'Peaks'.  These peaks are particularly important in Chromatin Immunoprecipiation experiments (ChIP-Seq or ChIP-Solexa experiments), as they indicate the location of a bound protein of interest.
+
|fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
 +
|-
 +
|[http://www.microbesonline.org/fasttree/ FastTree]
 +
|2.1.10-IGB-gcc-4.9.4<br>2.1.11-IGB-gcc-8.2.0
 +
|FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
 +
|-
 +
|[http://hannonlab.cshl.edu/fastx_toolkit/ FASTX-Toolkit]
 +
|0.0.14-IGB-gcc-4.9.4
 +
|The FASTX-Toolkit is a collection of command line tools for  Short-Reads FASTA/FASTQ files preprocessing. - Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
 +
|-
 +
|[https://github.com/adrianlopezroche/fdupes fdupes]
 +
|1.6.1-IGB-gcc-4.9.4
 +
|FDUPES is a program for identifying duplicate files residingwithin specified directories.
 +
|-
 +
|[https://github.com/tderrien/FEELnc FEELnc]
 +
|20180117-IGB-gcc-4.9.4
 +
|This document is intended to give a technical description of the FEELnc pipeline in order to annotate long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data (either with or without a reference genome).
 +
|-
 +
|fermi-lite
 +
|
 +
|Standalone C library for assembling Illumina short reads in small regions.
 +
|-
 +
|[https://www.ffmpeg.org/ FFmpeg]
 +
|3.3-IGB-gcc-4.9.4<br>4.4-IGB-gcc-8.2.0
 +
|A complete, cross-platform solution to record, convert and stream audio and video.
 +
|-
 +
|FFTW
 +
|
 +
|FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
 +
|-
 +
|[http://fulcrumgenomics.github.io/fgbio/ fgbio]
 +
|0.6.0-Java-1.8.0_152
 +
|fgbio is a command line toolkit for working with genomic and particularly next generation sequencing data.
 +
|-
 +
|[https://github.com/Zymo-Research/figaro figaro]
 +
|1.1.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.
 +
|-
 +
|file
 +
|
 +
|The file command is a file type guesser, that is, a command-line tool that tells you in words what kind of data a file contains.
 +
|-
 +
|[https://github.com/rrwick/Filtlong Filtlong]
 +
|0.2.1-IGB-gcc-8.2.0
 +
|Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
 +
|-
 +
|[https://github.com/ay-lab/fithic fithic]
 +
|2.0.7-IGB-gcc-8.2.0-Python-3.7.2
 +
|Fit-Hi-C (or FitHiC) was initially developed by Ferhat Ay, Timothy Bailey, and William Noble January 19th, 2014.
 +
|-
 +
|[https://xiph.org/flac/ FLAC]
 +
|1.3.1-IGB-gcc-4.9.4
 +
|Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.
 +
|-
 +
|[https://github.com/BrooksLabUCSC/flair/ flair]
 +
|1.5-IGB-gcc-8.2.0-Python-3.7.2
 +
|FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
 +
|-
 +
|[https://github.com/dstreett/FLASH2 FLASH2]
 +
|2.2.00-IGB-gcc-4.9.4
 +
|FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast toolto merge paired-end reads that were generated from DNA fragments whoselengths are shorter than twice the length of reads.  Merged read pairs resultin unpaired longer reads, which are generally more desired in genomeassembly and genome analysis processes.
 +
|-
 +
|flex
 +
|
 +
|Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.
 
|-
 
|-
 
|[https://github.com/seqan/flexbar flexbar]
 
|[https://github.com/seqan/flexbar flexbar]
−
|2.5-beta, 2.7
+
|3.0.3-IGB-gcc-4.9.4
−
|Flexbar — flexible barcode and adapter removal
+
|The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided.
 +
|-
 +
|[https://github.com/fenderglass/Flye Flye]
 +
|2.4.2-IGB-gcc-4.9.4-Python-2.7.13<br>2.7-IGB-gcc-4.9.4-Python-3.6.1<br>2.7.1-IGB-gcc-8.2.0-Python-3.7.2<br>2.8.1-IGB-gcc-8.2.0-Python-3.7.2<br>2.8.2-IGB-gcc-8.2.0-Python-3.7.2<br>2.9-IGB-gcc-8.2.0-Python-3.7.2<br>2.9.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
 +
|-
 +
|[https://github.com/steineggerlab/foldseek foldseek]
 +
|8-ef4e960
 +
|Foldseek enables fast and sensitive comparisons of large structure sets.
 +
|-
 +
|[https://foldxsuite.crg.eu/ foldx]
 +
|5.0
 +
|The FoldX Suite builds on the strong fundament of advanced protein design features, already implemented in the successful FoldX3, and exploits the power of fragment libraries, by integrating in silico digested backbone protein fragments of different lengths. S
 +
|-
 +
|fontconfig
 +
|
 +
|Fontconfig is a library designed to provide system-wide font configuration, customization andapplication access.
 +
|-
 +
|[https://github.com/Discngine/fpocket fpocket]
 +
|3.1.3-IGB-gcc-4.9.4
 +
|fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.
 
|-
 
|-
−
|[http://omics.informatics.indiana.edu/FragGeneScan/ FragGeneScan]
+
|[https://omics.informatics.indiana.edu/FragGeneScan/ FragGeneScan]
−
|1.19
+
|1.31-IGB-gcc-4.9.4
 
|FragGeneScan is an application for finding (fragmented) genes in short reads.
 
|FragGeneScan is an application for finding (fragmented) genes in short reads.
 
|-
 
|-
−
|[https://github.com/ekg/freebayes freebayes]
+
|[https://github.com/ekg/freebayes FreeBayes]
−
|0.9.6
+
|1.1.0-IGB-gcc-4.9.4<br>1.3.4-IGB-gcc-8.2.0
−
|FreeBayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.
+
|a haplotype-based variant detector
 +
|-
 +
|[http://freeimage.sourceforge.net FreeImage]
 +
|3.18.0-IGB-gcc-4.9.4
 +
|FreeImage is an Open Source library project for developers who would like to support popular graphicsimage formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy touse, fast, multithreading safe.
 +
|-
 +
|freetype
 +
|
 +
|FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
 +
|-
 +
|FriBidi
 +
|
 +
|The Free Implementation of the Unicode Bidirectional Algorithm.
 +
|-
 +
|[http://fureylab.web.unc.edu/software/fseq/ fseq]
 +
|1.84-Java-1.8.0_152
 +
|Tag sequencing using high-throughput sequencing technologies are now regularly employed to identify specific sequence features such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq).
 +
|-
 +
|[https://www.gams.com/ GAMS]
 +
|23.6.5<br>32.2.0
 +
|The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization. It consists of a language compiler and a stable of integrated high-performance solvers.
 +
|-
 +
|[https://github.com/lczech/gappa gappa]
 +
|0.6.1-IGB-gcc-8.2.0
 +
|gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data is typically produced by tools like EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files.
 +
|-
 +
|[https://github.com/simoncchu/GAPPadder GAPPadder]
 +
|20170601-IGB-gcc-4.9.4
 +
|GAPPadder is designed for closing gaps on the draft genomes with paired-end reads or mate-paired reads.
 +
|-
 +
|[https://github.com/jotech/gapseq gapseq]
 +
|1.1-IGB-gcc-8.2.0
 +
|Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
 +
|-
 +
|[http://www.broadinstitute.org/gatk/ GATK]
 +
|3.7-Java-1.8.0_121<br>3.8-0-Java-1.8.0_121<br>3.8-0-Java-1.8.0_152<br>3.8-1-0-Java-1.8.0_152<br>4.0.4.0-IGB-gcc-4.9.4-Java-1.8.0_152-Python-3.6.1<br>4.0.9.0-IGB-gcc-4.9.4-Java-1.8.0_152-Python-3.6.1<br>4.1.4.0-Java-1.8.0_152<br>4.2.4.1-Java-1.8.0_201<br>4.2.6.1-Java-1.8.0_201<br>4.4.0.0-Java-17.0.6
 +
|Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
 +
|-
 +
|[https://gaussian.com/gaussian16/ Gaussian]
 +
|16.C.01
 +
|Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling. Gaussian 16 is licensed for a wide variety of computer systems. All versions of Gaussian 16 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.
 +
|-
 +
|[https://github.com/halelab/GBS-SNP-CROP GBS-SNP-CROP]
 +
|4.0-IGB-gcc-4.9.4
 +
|The GBS SNP Calling Reference Optional Pipeline (GBS-SNP-CROP) is executed via a sequence of seven Perl scripts that integrate custom parsing and filtering procedures with well-known, vetted bioinformatic tools, giving the user full access to all intermediate files.
 
|-
 
|-
−
|fsl
+
|[https://github.com/GenomicsCoreLeuven/GBSX GBSX]
−
|5.0.8, 5.0.8(41)
+
|1.3-IGB-gcc-8.2.0-Java-1.8.0_201
−
|ERROR:102: Tcl command execution failed: setenv DYLD_LIBRARY_PATH $::env(LD_LIBRARY_PATH)
+
|Genotyping by Sequencing is an emerging technology for cost effective variant discovery and genotyping. However, current analysis tools do not fulfill all experimental design and analysis needs.
 
|-
 
|-
−
|[http://www.gams.com/ gams]
+
|GCC
−
|24.2
+
|
−
|The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization. It consists of a language compiler and a stable of integrated high-performance solvers. GAMS is tailored for complex, large scale modeling applications, and allows you to build large maintainable models that can be adapted quickly to new situations.
+
|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
 
|-
 
|-
−
|[http://www.broadinstitute.org/gatk gatk]
+
|GCCcore
−
|1.6-5, 1.6-13, 2.5-2, 2.6-4, 3.2-2, 3.3-0, 3.4-0, 3.5, 3.6
+
|
−
|The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
+
|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
 
|-
 
|-
−
|[http://gcc.gnu.org gcc]
+
|[https://github.com/fanagislab/GCE gce]
−
|4.8.1, 4.9.3
+
|1.0.2-IGB-gcc-8.2.0
−
|The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...). GCC was originally written as the compiler for the GNU operating system. The GNU system was developed to be 100% free software, free in the sense that it respects the user's freedom.
+
|GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencingsample
 
|-
 
|-
−
|[http://www.gdal.org/ gdal]
+
|[https://yanglab.westlake.edu.cn/software/gcta gcta]
−
|1.10.1, 1.11.2
+
|1.94.0Beta
−
|is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats.
+
|GCTA (Genome-wide Complex Trait Analysis) is a software package initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been greatly extended for many other analyses of data from genome-wide association studies (GWASs).
 
|-
 
|-
−
|[https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool gdc-client]
+
|[http://search.cpan.org/~lds/GD/ GD]
−
|1.0.1
+
|2.66-IGB-gcc-4.9.4-Perl-5.24.1<br>2.73-IGB-gcc-8.2.0-Perl-5.28.1
−
|The raw sequence files, typically stored as BAM or FASTQ, make up the bulk of data. The size for a single file can vary greatly depending on the specific analysis; However, some of the whole genome BAM files in The Cancer Genome Atlas (TCGA) reach sizes of 200-300 GB. In such cases, a high performance data download and submission client is essential.
+
|GD.pm - Interface to Gd Graphics Library
 +
|-
 +
|[http://www.gdal.org/ GDAL]
 +
|2.3.1-IGB-gcc-4.9.4<br>3.0.3-IGB-gcc-8.2.0
 +
|GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
 
|-
 
|-
−
|[http://genome.crg.es/software/geneid/index.html geneid]
+
|[http://www.gnu.org/software/gdb/gdb.html gdb]
−
|1.0, 1.4.4
+
|8.0.1-IGB-gcc-4.9.4-Python-2.7.13
−
|geneid is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure.
+
|The GNU Project Debugger
 
|-
 
|-
−
|[http://exon.gatech.edu/genemark/ GeneMark]
+
|[https://gdc.cancer.gov/access-data/gdc-data-transfer-tool gdc-client]
−
|4.32
+
|1.3.0-IGB-gcc-4.9.4-Python-2.7.13
−
|Novel genomic sequences can be analyzed either by the self-training program GeneMarkS (sequences longer than 50 kb) or by GeneMark.hmm with Heuristic models. For many species pre-trained model parameters are ready and available through the GeneMark.hmm page. Metagenomic sequences can be analyzed by MetaGeneMark , the program optimized for speed.
+
|The GDC Data Transfer Tool Client provides a command-line interface supporting both GDC data downloads and submissions.
 
|-
 
|-
−
|[http://brendelgroup.org/bioinformatics2go/GeneSeqer.php GeneSeqer]
+
|Gdk-Pixbuf
−
|20140226
+
|
−
|Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.
+
|The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
 
|-
 
|-
−
|[https://cghub.ucsc.edu/software/downloads.html genetorrent]
+
|[http://www1.montpellier.inra.fr/CBGP/software/GeneClass/ geneclass]
−
|3.8.7
+
|2.0
−
|CGHub provides binary and source distributions of the GeneTorrent client software for downloading sequence data from CGHub's repository.
+
|GeneClass2 is a program employing multilocus genotypes to select or exclude populations as origins of individuals (Assignment and Migrants Detection). This is a completely rewritten new version that includes pop100gene features.
 
|-
 
|-
−
|[https://www.gnu.org/software/gengetopt/gengetopt.html gengetopt]
+
|[http://exon.gatech.edu/GeneMark/ GeneMark-ES]
−
|2.22.6
+
|4.33-IGB-gcc-4.9.4-Perl-5.24.1<br>4.33-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded<br>4.62-IGB-gcc-8.2.0-Perl-5.28.1
−
|Gengetopt is a tool to write command line option parsing code for C programs.
+
|Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training.
 
|-
 
|-
−
|[https://github.com/michaelbarton/genomer genomer]
+
|[http://exon.gatech.edu/GeneMark/ GeneMarkS]
−
|0.0.10
+
|4.30-IGB-gcc-4.9.4
−
|Genomer is command line glue for genome projects. I wrote this tool to simplify the small but tedious tasks required when finishing a genome. Genomer does not perform assembly, gap closing or genome annotation. Genomer does however make it easy to reorganise contigs in a genome, map annotations on to the genome and generate the files required to submit a genome.
+
|GeneMarkS: a self-training method for prediction of gene starts in microbial genomes
 +
|-
 +
|[http://topaz.gatech.edu/GeneMark/ GeneMarkS-T]
 +
|5.1
 +
|
 +
|-
 +
|gengetopt
 +
|
 +
|Gengetopt is a tool to write command line option parsing code for C programs. - Homepage: https://www.gnu.org/software/gengetopt/gengetopt.html
 +
|-
 +
|[http://genomethreader.org/ GenomeThreader]
 +
|1.7.1
 +
|GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. GenomeThreader was motivated by disabling limitations in GeneSeqer, a popular gene prediction program which is widely used for plant genome annotation.
 
|-
 
|-
 
|[http://genometools.org/ genometools]
 
|[http://genometools.org/ genometools]
−
|1.5.1, 1.5.2, 1.5.7
+
|1.5.10-IGB-gcc-4.9.4
 
|The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
 
|The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
 
|-
 
|-
−
|gerp
+
|[https://github.com/PacificBiosciences/GenomicConsensus GenomicConsensus]
−
|jun-11-2014(20)
+
|2.3.3
−
|ERROR:102: Tcl command execution failed: set _description "GERP identifies constrained elements in multiple alignments by quantifying substitution deficits. These deficits represent substitutions that would have occurred if the element were neutral DNA, but did not occur because the element has been under functional constraint. We refer to these deficits as "Rejected Substitutions". Rejected substitutions are a natural measure of constraint that reflects the strength of past purifying selection on the element."
+
|The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.
 +
|-
 +
|[https://github.com/jsh58/Genrich genrich]
 +
|0.6-IGB-gcc-8.2.0
 +
|Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.
 +
|-
 +
|[http://trac.osgeo.org/geos geos]
 +
|3.7.1-IGB-gcc-4.9.4
 +
|GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite
 +
|-
 +
|GEOS
 +
|
 +
|GEOS (Geometry Engine - Open Source) is a C++ port of the  Java Topology Suite (JTS)
 +
|-
 +
|gettext
 +
|
 +
|GNU gettext is an important step for the GNU Translation Project, as it is an asset on which we maybuild many other steps. This package offers to programmers, translators, and even users, a well integrated set of toolsand documentation
 
|-
 
|-
 
|[http://acgt.cs.tau.ac.il/gevalt/ gevalt]
 
|[http://acgt.cs.tau.ac.il/gevalt/ gevalt]
−
|2.0
+
|2.0-Java-1.8.0_152
−
|GEVALT (GEnotype Visualization and ALgorithmic Tool) is designed to simplify and expedite the process of genotype analysis and disease association tests by providing a common interface to several common tasks relating to such analyses. It is aimed for analysis of unrelated individuals as well as two-generation families.
+
|GEVALT (GEnotype Visualization and ALgorithmic Tool) is designed to simplify and expedite the process of genotype analysis and disease association tests by providing a common interface to several common tasks relating to such analyses.
 +
|-
 +
|[https://github.com/lh3/gfatools gfatools]
 +
|0.4-IGB-gcc-4.9.4
 +
|gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED.
 +
|-
 +
|[https://github.com/billzt/gff3sort gff3sort]
 +
|1.0.0-IGB-gcc-4.9.4-Perl-5.24.1
 +
|A Perl Script to sort gff3 files and produce suitable results for tabix tools
 +
|-
 +
|[http://ccb.jhu.edu/software/stringtie/gffcompare.shtml gffcompare]
 +
|0.10.6-IGB-gcc-4.9.4
 +
|The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the query files), when compared with a reference annotation (also provided as GFF).
 +
|-
 +
|[http://ccb.jhu.edu/software/stringtie/gff.shtml gffread]
 +
|ba7535f-IGB-gcc-4.9.4
 +
|The program gffread can be used to validate, filter, convert and perform various other operations on GFF files
 +
|-
 +
|gffutils
 +
|0.10.1-IGB-gcc-8.2.0-Python-3.7.2<br>0.11.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|
 +
|-
 +
|[https://github.com/gflags/gflags gflags]
 +
|2.2.2-IGB-gcc-4.9.4<br>2.2.2-IGB-gcc-8.2.0
 +
|The gflags package contains a C++ library that implements commandline flagsprocessing.  It includes built-in support for standard types such as stringand the ability to define flags in the source file in which they are used.
 +
|-
 +
|[https://bitbucket.org/feeldead/gfold GFOLD]
 +
|1.1.4-IGB-gcc-4.9.4
 +
|GFOLD stands for Generalized FOLD change for ranking differentially expressed genes from RNA-seq data. GFOLD is especially useful when no replicate is available. GFOLD generalizes the fold change by considering the posterior distribution of log fold change, such that each gene is assigned a reliable fold change.
 +
|-
 +
|[http://ghostscript.com GhostScript]
 +
|9.21-IGB-gcc-4.9.4<br>9.55.0-IGB-gcc-8.2.0
 +
|Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
 +
|-
 +
|[http://git-scm.com/ git]
 +
|2.28.0-IGB-gcc-8.2.0<br>2.9.5-IGB-gcc-4.9.4
 +
|Git is a free and open source distributed version control system designedto handle everything from small to very large projects with speed and efficiency.
 +
|-
 +
|[https://git-lfs.github.com/ git-lfs]
 +
|2.2.1-IGB-gcc-4.9.4
 +
|Git Large File Storage (LFS) replaces large files such as audio samples, videos,  datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server  like GitHub.com or GitHub Enterprise.
 +
|-
 +
|[http://glew.sourceforge.net/ glew]
 +
|2.1.0-IGB-gcc-4.9.4
 +
|The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-sourceC/C++ extension loading library. GLEW provides efficient run-time mechanismsfor determining which OpenGL extensions are supported on the target platform.
 +
|-
 +
|GLib
 +
|
 +
|GLib is one of the base libraries of the GTK+ project
 +
|-
 +
|[http://www.cbcb.umd.edu/software/glimmer/ GLIMMER]
 +
|3.02b-IGB-gcc-4.9.4
 +
|Glimmer is a system for finding genes in microbial DNA, especiallythe genomes of bacteria, archaea, and viruses.
 +
|-
 +
|[https://ccb.jhu.edu/software/glimmerhmm GlimmerHMM]
 +
|3.0.4-IGB-gcc-4.9.4
 +
|GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.
 +
|-
 +
|[https://docs.globus.org/cli/ globus-cli]
 +
|3.10.1-IGB-gcc-8.2.0-Python-3.7.2<br>3.18.0-IGB-gcc-8.2.0-Python-3.7.2
 +
|The CLI provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.
 +
|-
 +
|[https://github.com/google/glog glog]
 +
|0.4.0-IGB-gcc-4.9.4<br>0.5.0-IGB-gcc-8.2.0
 +
|A C++ implementation of the Google logging module.
 
|-
 
|-
−
|[http://bioinfo.icgeb.res.in/gff/ gff]
+
|glproto
−
|2.1
+
|
−
|GFF-Ex, a Genome Feature extraction package extracts Gene, Exon, Intron, Upstream Region of Gene (Promoters), Intergenic and CDS/cDNA sequences by just tweeting in the Genome Feature File (gff) along with the corresponding genome/chromosome sequence. GFF-Ex. is a fusion of shell and Perl, developed for platforms supporting UNIX based file system.
+
|X protocol and ancillary headers
 
|-
 
|-
−
|[http://github.com/gpertea/gffcompare gffcompare]
+
|[http://research-pub.gene.com/gmap/ GMAP]
−
|0.9.7
+
|2018-05-30-IGB-gcc-4.9.4<br>2020-06-04-IGB-gcc-8.2.0
−
|compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples). classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format)
+
|A Genomic Mapping and Alignment Program for mRNA and EST Sequences, andGSNAP: Genomic Short-read Nucleotide Alignment Program
 
|-
 
|-
−
|[https://pythonhosted.org/gffutils/index.html gffutils]
+
|[http://research-pub.gene.com/gmap/ GMAP-GSNAP]
−
|0.8.3, 0.8.4
+
|2017-11-15-IGB-gcc-4.9.4
−
|gffutils is a Python package for working with GFF and GTF files in a hierarchical manner. It allows operations which would be complicated or time-consuming using a text-file-only approach.
+
|GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
 
|-
 
|-
−
|[https://www.gnu.org/software/libc/ glibc]
+
|GMP
−
|2.14, 2.14.1
+
|
−
|The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems
+
|GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
 
|-
 
|-
−
|[https://ccb.jhu.edu/software/glimmer/ glimmer]
+
|[https://melodi.ee.washington.edu/gmtk/ GMTK]
−
|3.02
+
|1.4.4-IGB-gcc-4.9.4
−
|Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. Glimmer (Gene Locator and Interpolated Markov ModelER) uses interpolated Markov models (IMMs) to identify the coding regions and distinguish them from noncoding DNA.
+
|The Graphical Models Toolkit (GMTK) is an open source, publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs). GMTK can be used for applications and research in speech and language processing, bioinformatics, activity recognition, and any time series application. GMTK has many features, including exact and approximate inference; a large variety of built-in factors including dense, sparse, and deterministic conditional probability tables, native support for ARPA backoff-based factors and factored language models, parameter sharing, gamma and beta distributions, dense and sparse Gaussian factors, heterogeneous mixtures, deep neural network factors, and time-inhomogeneous trellis factors; arbitrary order embedded Markov chains; a GUI-based graph viewer; flexible feature-file support and processing tools (supporting pfiles, HTK files, ASCII/binary, and HDF5 files); and both offline and streaming online inference methods that can be used for both parameter learning and prediction. More information is available in the documentation. All in all, GMTK offers a flexible, concise, and expressive probabilistic modeling framework with which one may rapidly specify a vast collection of temporal statistical models.
 
|-
 
|-
−
|[http://research-pub.gene.com/gmap/ gmap]
+
|[http://gnuplot.sourceforge.net/ gnuplot]
−
|2011-09-14, 2013-03-31, 2016-09-23
+
|4.6.7-IGB-gcc-4.9.4<br>4.6.7-IGB-gcc-8.2.0<br>5.0.6-IGB-gcc-4.9.4
−
|GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences
+
|Portable interactive, function plotting utility
 
|-
 
|-
−
|[http://topaz.gatech.edu/GeneMark/gmes_instructions.html gmes]
+
|GObject-Introspection
−
|v2.3e
+
|
−
|Unsupervised training is an important feature of the GeneMark-ES algorithm that identifies protein coding genes in eukaryotic genomes. This is the only eukaryotic gene finder that can perform gene prediction without curated training sets.
+
|GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
 
|-
 
|-
−
|gmp
+
|[https://github.com/cov-ert/gofasta gofasta]
−
|6.0.0
+
|0.0.3
−
|gmp needed gfor gcc compile Homepage:
+
|Gofasta uses a slightly modified version of the bit-level coding scheme for nucleotides by Emmanuel Paradis (described here, and implemented in the R package ape).
 
|-
 
|-
−
|[https://gnupg.org gnupg]
+
|gompi
−
|2.0.22
+
|
−
|GnuPG is a complete and free implementation of the OpenPGP standard as defined by RFC4880 (also known as PGP). GnuPG allows to encrypt and sign your data and communication, features a versatile key management system as well as access modules for all kinds of public key directories. GnuPG, also known as GPG, is a command line tool with features for easy integration with other applications. A wealth of frontend applications and libraries are available. GnuPG also provides support for S/MIME and Secure Shell (ssh).
+
|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
 
|-
 
|-
−
|[http://www.gnuplot.info/ gnuplot]
+
|[https://github.com/data61/gossamer gossamer]
−
|4.6.3
+
|20170105-IGB-gcc-4.9.4
−
|Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms
+
|The gossamer bioinformatics suite contains goss, gossple, xenome, and electus
 
|-
 
|-
 
|[https://www.gnu.org/software/gperf/ gperf]
 
|[https://www.gnu.org/software/gperf/ gperf]
−
|3.0.4
+
|3.1-IGB-gcc-4.9.4<br>3.1-IGB-gcc-8.2.0
−
|GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
+
|GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
 +
|-
 +
|[https://gradle.org Gradle]
 +
|4.7
 +
|Complete Gradle install.From mobile apps to microservices, from small startups to big enterprises,Gradle helps teams build, automate and deliver better software, faster.  
 
|-
 
|-
−
|[https://huttenhower.sph.harvard.edu/graphlan graphlan]
+
|[http://www.graphicsmagick.org/ GraphicsMagick]
−
|1.0
+
|1.3.26-IGB-gcc-4.9.4
−
|GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. GraPhlAn focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
+
|GraphicsMagick is the swiss army knife of image processing.
 +
|-
 +
|[https://bitbucket.org/nsegata/graphlan/ graphlan]
 +
|6ca8735-IGB-gcc-4.9.4-Python-2.7.13
 +
|GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
 +
|-
 +
|[https://github.com/DecodeGenetics/graphtyper graphtyper]
 +
|1.3-IGB-gcc-4.9.4
 +
|Graphtyper is a highly scalable genotyping software. It represents a reference genome and known variants of a genomic region using an acyclic mathematical graph structure (a "pangenome reference"), which high-throughput sequence reads are re-aligned to for the purpose of discovering and genotyping SNPs and small indels.
 
|-
 
|-
−
|[http://www-graphviz.org graphviz]
+
|[http://www.graphviz.org/ graphviz]
−
|2.32.0
+
|2.40.1-IGB-gcc-4.9.4<br>2.40.1-IGB-gcc-4.9.4-Python-2.7.13
 
|Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics,  software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
 
|Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics,  software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
 
|-
 
|-
−
|[http://minillinim.github.io/GroopM/ groopm]
+
|[https://sourceforge.net/projects/biogrinder/ Grinder]
−
|0.2.10.19, 0.3.4
+
|0.5.4-IGB-gcc-4.9.4-Perl-5.24.1
−
|GroopM is a metagenomic binning toolset. It leverages spatio-temoral dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets.
+
|Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
 
|-
 
|-
−
|[http://www.gnu.org/software/gsl/ gsl]
+
|[https://www.gromacs.org/ GROMACS]
−
|1.16
+
|2021.2-IGB-gcc-8.2.0<br>2021.2-IGB-gcc-8.2.0-CUDA-11.1.0
−
|The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.  The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
+
|GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
 +
|-
 +
|GSL
 +
|
 +
|The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
 +
|-
 +
|[https://cloud.google.com/storage/docs/gsutil gsutil]
 +
|4.52-IGB-gcc-4.9.4-Python-3.6.1
 +
|gsutil is a Python application that lets you access Cloud Storage from the command line.
 +
|-
 +
|[https://ecogenomics.github.io/GTDBTk/ GTDBTk]
 +
|1.5.0<br>2.1.1<br>2.3.0
 +
|GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB
 +
|-
 +
|[https://github.com/google/googletest gtest]
 +
|1.8.0-IGB-gcc-4.9.4
 +
|Googles C++ test framework
 +
|-
 +
|[https://developer.gnome.org/gtk+/stable/ GTK+]
 +
|2.24.31-IGB-gcc-4.9.4-Python-2.7.13<br>2.24.31-IGB-gcc-4.9.4-Python-3.6.1<br>2.24.31-IGB-gcc-8.2.0-Python-3.7.2
 +
|The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
 
|-
 
|-
 
|[http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html gtool]
 
|[http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html gtool]
 
|0.7.5
 
|0.7.5
−
|GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
+
|GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
 +
|-
 +
|[http://guidance.tau.ac.il/ver2/ GUIDANCE]
 +
|2.02-IGB-gcc-4.9.4-Perl-5.24.1
 +
|GUIDANCE is meant to be used for weighting, filtering or masking unreliably aligned positions in sequence alignments before subsequent analysis. For example, align codon sequences (nucleotide sequences that code for proteins) using PAGAN, remove columns with low GUIDANCE scores, and use the remaining alignment to infer positive selection using the branch-site dN/dS test. Other analyses where GUIDANCE filtering could be useful include phylogeny reconstruction, reconstruction of the history of specific insertion and deletion events, inference of recombination events, etc. - Homepage: http://guidance.tau.ac.il/ver2/
 +
|-
 +
|[https://github.com/tsailabSJ/guideseq guideseq]
 +
|20190913-IGB-gcc-8.2.0-Python-3.7.2
 +
|The guideseq package implements our data preprocessing and analysis pipeline for GUIDE-Seq data. It takes raw sequencing reads (FASTQ) and a parameter manifest file (.yaml) as input and produces a table of annotated off-target sites as output.
 +
|-
 +
|[https://community.nanoporetech.com/posts/pre-release-of-stand-alone guppy]
 +
|2.1.3<br>2.2.2<br>2.3.1<br>2.3.7<br>3.0.3<br>3.1.5<br>3.2.2<br>3.4.3
 +
|Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.
 +
|-
 +
|[https://community.nanoporetech.com/posts/pre-release-of-stand-alone guppy-gpu]
 +
|2.3.1<br>2.3.5<br>2.3.7<br>3.0.3<br>3.1.5<br>3.2.2<br>3.4.3<br>3.5.2<br>3.6.0<br>4.0.11<br>4.0.15<br>4.2.2<br>4.5.3<br>5.0.16
 +
|Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.  
 
|-
 
|-
−
|[http://guidance.tau.ac.il/ver2/ guidance]
+
|[http://www.gurobi.com/ Gurobi]
−
|2.01
+
|7.5.2
−
|GUIDANCE is meant to be used for weighting, filtering or masking unreliably aligned positions in sequence alignments before subsequent analysis. For example, align codon sequences (nucleotide sequences that code for proteins) using PAGAN, remove columns with low GUIDANCE scores, and use the remaining alignment to infer positive selection using the branch-site dN/dS test. Other analyses where GUIDANCE filtering could be useful include phylogeny reconstruction, reconstruction of the history of specific insertion and deletion events, inference of recombination events, etc.
+
|The Gurobi Optimizer was designed from the ground up to be the fastest, most powerful solver available for your LP, QP, QCP, and MIP (MILP, MIQP, and MIQCP) problems.
 
|-
 
|-
−
|[https://sites.google.com/site/gvcftools/home gvcftools]
+
|[https://github.com/Gaius-Augustus/GUSHR GUSHR]
−
|0.16
+
|20200928-Java-1.8.0_201
−
|gvcftools is a set of utilities to help create and analyze Genome VCF (gVCF) files.
+
|Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation.
 
|-
 
|-
−
|[https://github.com/Illumina/hap.py/tree/ee33640b218b5c575e999be619884992781ab9ac hap.py]
+
|[https://www.aaronrenn.com/arenn/hacking/gzrt/gzrt.html gzrt]
−
|0.3.0
+
|0.8-IGB-gcc-8.2.0
−
|This is a set of programs based on htslib to compare VCF files by specified haplotype.
+
|So you thought you had your files backed up - until it came time to restore. Then you found out that you had bad sectors and you've lost almost everything because gzip craps out 10% of the way through your archive. The gzip Recovery Toolkit has a program - gzrecover - that attempts to skip over bad data in a gzip archive. This saved me from exactly the above situation. Hopefully it will help you as well.  
 
|-
 
|-
−
|[http://www.brown.edu/Research/Istrail_Lab/hapcompass.php hapcompass]
+
|[https://cran.r-project.org/web/packages/h2o/index.html h2o]
−
|0.7.5
+
|3.14.0.3-IGB-gcc-4.9.4-R-3.3.3
−
|HAPCOMPASS: A fast cycle basis algorithm for accurate haplotype assembly of sequence data. HapCompass for polyploid genomes can currently be used to create accurate pairwise SNP phasings. However, it currently only produces an entire haplotype assembly that is consistent with the data. We are currently working on modifying the algorithm to produce the best haplotype assembly given the resolved compass graph.
+
|R scripting functionality for H2O, the open source math engine for big data that computes parallel distributed machine learning algorithms such as generalized linear models, gradient boosting machines, random forests, and neural networks (deep learning) within various cluster environments.
 +
|-
 +
|h5py
 +
|
 +
|a toolkit for working with nanopore sequencing data from Oxford Nanopore.
 +
|-
 +
|[https://forge-dga.jouy.inra.fr/projects/hapflk hapflk]
 +
|1.4-IGB-gcc-4.9.4-Python-3.6.1
 +
|hapflk is a software implementing the hapFLK and FLK tests for the detection of selection signatures based on multiple population genotyping data.
 +
|-
 +
|[https://github.com/institut-de-genomique/HAPO-G HAPO-G]
 +
|1.2-IGB-gcc-8.2.0
 +
|Hapo-G (pronounced like apogee) is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.
 +
|-
 +
|HarfBuzz
 +
|
 +
|HarfBuzz is an OpenType text shaping engine.
 +
|-
 +
|[http://www.hdfgroup.org/HDF5/ HDF5]
 +
|1.8.12-IGB-gcc-4.9.4<br>1.8.18-IGB-gcc-4.9.4<br>1.8.18-IGB-gcc-8.2.0
 +
|HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
 
|-
 
|-
−
|[http://www.hdfgroup.org/products/hdf4/ hdf4]
+
|help2man
−
|4.2.10
+
|
−
|HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. There are two versions of HDF: HDF4 and HDF5. HDF4 is the first HDF format. Although HDF4 is still funded, new users that are not constrained to using HDF4, should use HDF5 .
+
|help2man produces simple manual pages from the --help and --version output of other commands.
 
|-
 
|-
−
|[http://www.hdfgroup.org/HDF5/ hdf5]
+
|[https://github.com/soedinglab/hh-suite hhsuite]
−
|1.8.11, 1.8.16
+
|3.2.0<br>3.3.0-IGB-gcc-8.2.0
−
|HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
+
|The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
 
|-
 
|-
 
|[https://github.com/nservant/HiC-Pro HiC-Pro]
 
|[https://github.com/nservant/HiC-Pro HiC-Pro]
−
|2.7.1
+
|3.1.0-IGB-gcc-8.2.0-Python-3.7.2
−
|HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro can analyse data from digestion protocols as well as data from protocols that do not require restriction enzyme such as DNase Hi-C.
+
|HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not require restriction enzyme such as DNase Hi-C.
 +
|-
 +
|[https://hicexplorer.readthedocs.io/en/latest/index.html HiCExplorer]
 +
|2.2.1.1-IGB-gcc-8.2.0-Python-3.7.2<br>3.7.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|HiCExplorer addresses the common tasks of Hi-C data analysis from processing to visualization.
 +
|-
 +
|[https://github.com/chhylp123/hifiasm hifiasm]
 +
|0.13-IGB-gcc-8.2.0<br>0.14.2-IGB-gcc-8.2.0<br>0.15-IGB-gcc-8.2.0<br>0.16.1-IGB-gcc-8.2.0<br>0.18.1-IGB-gcc-8.2.0<br>0.19.5-IGB-gcc-8.2.0<br>0.19.6-IGB-gcc-8.2.0<br>0.5-IGB-gcc-8.2.0
 +
|Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome. Thus, it is able to keep the haplotype information as much as possible.
 +
|-
 +
|[https://github.com/xfengnefx/hifiasm-meta hifiasm-meta]
 +
|0.3-IGB-gcc-8.2.0
 +
|A hifiasm fork for metagenome assembly using Hifi reads
 +
|-
 +
|[https://github.com/higlass/higlass-python higlass-python]
 +
|0.4.4-IGB-gcc-8.2.0-Python-3.7.2
 +
|Python bindings to the HiGlass for tile serving, view config generation, and Jupyter Notebook + Lab integration.
 +
|-
 +
|[https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]
 +
|2.0.5-IGB-gcc-4.9.4<br>2.1.0-IGB-gcc-4.9.4<br>2.2.0-IGB-gcc-4.9.4<br>2.2.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
 +
|-
 +
|[http://daehwankimlab.github.io/hisat2/hisat-3n/ HISAT2-3N]
 +
|20221013-IGB-gcc-8.2.0-Python-3.7.2
 +
|HISAT-3N (hierarchical indexing for spliced alignment of transcripts - 3 nucleotides) is designed for nucleotide conversion sequencing technologies and implemented based on HISAT2.
 +
|-
 +
|[http://hmmer.org/ HMMER]
 +
|2.3.2-IGB-gcc-4.9.4<br>2.3.2-IGB-gcc-8.2.0<br>3.1b2-IGB-gcc-4.9.4<br>3.2.1-IGB-gcc-4.9.4<br>3.3.1-IGB-gcc-8.2.0
 +
|HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).  Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
 +
|-
 +
|[http://homer.ucsd.edu/homer/ HOMER]
 +
|4.9.1-IGB-gcc-4.9.4-Perl-5.24.1
 +
|HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.
 +
|-
 +
|[https://github.com/rhuebler/HOPS HOPS]
 +
|0.33
 +
|HOPS is a java pipeline which focuses on screening MALT data for the presence of a user-specified list of target species. The pipeline essentially exists to make it easier to use MALT and MaltExtract in unison.
 
|-
 
|-
−
|[https://ccb.jhu.edu/software/hisat2/index.shtml hisat2]
+
|[https://hisham.hm/htop/ htop]
−
|2.0.4
+
|2.2.0-IGB-gcc-4.9.4
−
|HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as against a single reference genome).
+
|This is htop, an interactive process viewer for Unix systems. It is a text-mode application (for console or X terminals) and requires ncurses.  
 
|-
 
|-
−
|hmmer-mpi
+
|[http://www-huber.embl.de/users/anders/HTSeq/ HTSeq]
−
|2.32-MPI-0.92
+
|0.12.4-IGB-gcc-8.2.0-Python-3.7.2<br>0.9.0-IGB-gcc-4.9.4-Python-2.7.13<br>0.9.1-IGB-gcc-4.9.4-Python-2.7.13
−
|adds environmental variables to hmmer-mpi
+
|A framework to process and analyze data from high-throughput sequencing (HTS) assays
 
|-
 
|-
−
|[http://hmmer.janelia.org/ hmmer]
+
|[http://www.htslib.org/ HTSlib]
−
|2.3.2, 3.0, 3.1b1, 3.1b2
+
|1.10.2-IGB-gcc-8.2.0<br>1.11-IGB-gcc-8.2.0<br>1.12-IGB-gcc-8.2.0<br>1.17-IGB-gcc-8.2.0<br>1.4-IGB-gcc-4.9.4<br>1.5-IGB-gcc-4.9.4<br>1.9-IGB-gcc-4.9.4<br>1.9-IGB-gcc-8.2.0
−
|HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs).
+
|A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
 
|-
 
|-
−
|[http://homer.salk.edu/homer/ HOMER]
+
|[https://github.com/biobakery/humann/ humann]
−
|4.7.2
+
|3.0.1-IGB-gcc-8.2.0-Python-3.7.2<br>3.1.1-IGB-gcc-8.2.0-Python-3.7.2<br>3.6-IGB-gcc-8.2.0-Python-3.7.2<br>3.7-IGB-gcc-8.2.0-Python-3.7.2
−
|HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and next-gen sequencing analysis. It is a collection of command line programs for unix-style operating systems written in Perl and C++. HOMER was primarily written as a de novo motif discovery algorithm and is well suited for finding 8-20 bp motifs in large scale genomics data. HOMER contains many useful tools for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets.
+
|HUMAnN (the HMP Unified Metabolic Analysis Network) is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.
 
|-
 
|-
−
|[http://www-huber.embl.de/users/anders/HTSeq/doc/overview.html htseq]
+
|[http://huttenhower.sph.harvard.edu/humann2 HUMAnN2]
−
|0.7.2
+
|0.11.1-IGB-gcc-4.9.4-Python-3.6.1<br>0.11.2-IGB-gcc-4.9.4-Python-3.6.1
−
|HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
+
|HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
 
|-
 
|-
−
|[http://www.htslib.org/ htslib]
+
|hwloc
−
|1.0, 1.3.2
+
|
−
|a C library for reading/writing high-throughput sequencing data
+
|The Portable Hardware Locality (hwloc) software package provides a portable abstraction(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, includingNUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers varioussystem attributes such as cache and memory information as well as the locality of I/O devices such asnetwork interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gatheringinformation about modern computing hardware so as to exploit it accordingly and efficiently.
 
|-
 
|-
−
|[http://huttenhower.sph.harvard.edu/humann humann]
+
|[https://github.com/kensung-lab/hypo hypo]
−
|0.99
+
|1.0.3-IGB-gcc-8.2.0
−
|HUMAnN is a pipeline for efficiently and accurately determining the presence/absence and abundance of microbial pathways in a community from metagenomic data.
+
|HyPo--a Hybrid Polisher-- utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. I
 
|-
 
|-
−
|[http://www.open-mpi.org/projects/hwloc/ hwloc]
+
|[https://pypi.org/project/iced/ iced]
−
|1.11.0
+
|0.5.10-IGB-gcc-8.2.0-Python-3.7.2
−
|The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading.
+
|ICE normalization
 
|-
 
|-
−
|[https://software.intel.com/en-us/intel-parallel-studio-xe icc]
+
|[http://icorn.sourceforge.net/documentation.html icorn]
−
|2013.5.192
+
|0.97-IGB-gcc-4.9.4
−
|Intel® Parallel Studio XE 2013 SP1 provides C/C++ and Fortran developers cutting edge performing compilers and libraries, the right parallel programming models, and complementary and compatible analysis tools.
+
|Inputs: Reference Sequence (FASTA) & reads (FASTQ) & information of short reads
 
|-
 
|-
−
|[http://i.cs.hku.hk/~alse/hkubrg/projects/idba_mt/index.html idba-mt]
+
|[https://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ idba-ud]
−
|20140307
+
|1.1.3-IGB-gcc-4.9.4
−
|IDBA-MT is an iterative De Bruijn Graph De Novo short read assembler for meta-transcriptome. It is purely de novo assembler based on paired-end RNA sequencing reads only. IDBA-MT is a post-processing software for IDBA-UD contigs for removing chimeria contigs and extending contig length using paired-end reads information.
+
|IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.  
 
|-
 
|-
−
|[http://i.cs.hku.hk/~alse/hkubrg/projects/idba/index.html idba]
+
|[https://github.com/kundajelab/idr IDR]
−
|1.1.0, 1.1.1
+
|2.0.4-IGB-gcc-4.9.4-Python-3.6.1
−
|IDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics. Most assemblers based on de Bruijn graph build a de Bruijn graph with a specific k to perform the assembling task.
+
|The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates. In laymans terms, the IDR method compares a pair of ranked lists of identifications (such as ChIP-seq peaks).
 
|-
 
|-
−
|[https://github.com/yuzhang123/IDEAS ideas]
+
|IGB-gcc
−
|1.05
+
|
−
|This program is designed to segment genomes in multiple cell types simultaneously so to better identify functional elements and epigenomic variation/conservation patterns, both globally and locally, across all cell types.
+
|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
 
|-
 
|-
−
|[http://www.broadinstitute.org/igv/ IGV]
+
|[http://software.broadinstitute.org/software/igv/ igv]
−
|2.1.24, 2.3.40, 2.3.68, 2.3.95
+
|2.4.4-Java-1.8.0_152<br>2.7.2-Java-11.0.5<br>2.8.0-Java-11.0.5<br>snapshot-Java-11.0.5
 
|The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
 
|The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
 
|-
 
|-
−
|[https://www.broadinstitute.org/igv/igvtools IGVTools]
+
|[https://databank.illinois.edu/ IllinoisDataBank]
−
|2.1.24, 2.3.68
+
|1.0-IGB-gcc-4.9.4-Python-3.6.1
−
|The igvtools utility provides a set of tools for pre-processing data files.
+
|The Illinois Data Bank is a public access repository for publishing research data from the University of Illinois at Urbana-Champaign
 
|-
 
|-
−
|[http://sourceforge.net/projects/image2/files/ IMAGE]
+
|[https://github.com/pjeraldo/imtornado2 IM-TORNADO]
−
|2.33
+
|2.0.3.3-IGB-gcc-4.9.4-Python-2.7.13
−
|IMAGE stands for Iterative Mapping and Assembly for Gap Elimination. It is a software designed to close gaps in any draft assembly using Illumina paired end reads.
+
|A pipeline for 16S reads from paired-end libraries
 
|-
 
|-
−
|[http://www.imagemagick.org ImageMagick]
+
|[http://www.imagemagick.org/ ImageMagick]
−
|6.7.8-9
+
|6.9.11-58-IGB-gcc-4.9.4<br>7.0.5-5-IGB-gcc-4.9.4
−
|ImageMagick® is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.
+
|ImageMagick is a software suite to create, edit, compose, or convert bitmap images
 
|-
 
|-
 
|[https://mathgen.stats.ox.ac.uk/impute/impute_v2.html impute2]
 
|[https://mathgen.stats.ox.ac.uk/impute/impute_v2.html impute2]
 
|2.3.2
 
|2.3.2
−
|IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes.
+
|IMPUTE2 is freely available for academic use. To see rules for non-academic use, please read the LICENCE file, which is included with each software download.
 +
|-
 +
|[http://eddylab.org/infernal/ Infernal]
 +
|1.1.2-IGB-gcc-4.9.4
 +
|Infernal,INFERence of RNA ALignment, is for searching DNA sequence databases for RNA structure and sequence similarities.
 +
|-
 +
|[https://www.ebi.ac.uk/interpro/interproscan.html InterProScan]
 +
|5.27-66.0-IGB-gcc-4.9.4-Java-1.8.0_152<br>5.28-67.0-IGB-gcc-4.9.4-Java-1.8.0_152<br>5.33-72.0-IGB-gcc-4.9.4-Java-1.8.0_152<br>5.33-72.0-IGB-gcc-4.9.4-Java-1.8.0_201<br>5.47-82.0-IGB-gcc-8.2.0-Java-15.0.1<br>5.56-89.0-IGB-gcc-8.2.0-Java-15.0.1
 +
|InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPros signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.
 +
|-
 +
|[https://intervene.readthedocs.io/en/latest/ intervene]
 +
|0.6.5
 +
|a tool for intersection and visualization of multiple genomic region sets
 +
|-
 +
|[https://github.com/LLNL/ior ior]
 +
|3.0.1-IGB-gcc-4.9.4
 +
|Parallel filesystem I/O benchmark
 +
|-
 +
|[https://ipyrad.readthedocs.io/en/latest/ ipyrad]
 +
|0.9.57
 +
|Welcome to ipyrad, an interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types. Please explore the documentation to find out more about the features of ipyrad.
 
|-
 
|-
−
|[http://infernal.janelia.org/ infernal]
+
|[http://ipython.org/index.html IPython]
−
|1.1, 1.1.1, 1.1rc1, 1.1rc2
+
|5.3.0-IGB-gcc-4.9.4-Python-3.6.1
−
|Infernal ('INFERence of RNA ALignment') is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs).
+
|IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.
 
|-
 
|-
−
|[http://inparanoid.sbc.su.se/cgi-bin/index.cgi inparanoid]
+
|[https://github.com/christophertbrown/iRep iRep]
−
|4.1
+
|20191228-IGB-gcc-8.2.0-Python-3.7.2
−
|The InParanoid program was developed at the Center for Genomics and Bioinformatics to address the need to identify orthologs. Homologs that originate from a speciation event are called orthologs and homologs that originate from a gene duplication event are called paralogs. If a duplication event predates the speciation event the parlogs are called outparalogs, and they can be present in different species. If instead an ortholog undegoes one or several duplication events, the resulting paralogs are called inparalogs, and they are co-orthologs to one or more orthologs in another species. Since an outparalog pair ought to have a more diversified function than inparalogs, it is useful to distinguish between the two. Furthermore, clustering inparalogs together allows proper identification of both one-to-one and many-to-many orthology cases.
+
|iRep is a method for determining replication rates for bacteria from single time point metagenomics sequencing and draft-quality genomes.
 
|-
 
|-
−
|[https://www.ebi.ac.uk/interpro/interproscan.html interproscan]
+
|[https://github.com/williamritchie/IRFinder IRFinder]
−
|5.19, 5.22-61.0
+
|1.3.1-IGB-gcc-8.2.0
−
|InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.
+
|Detecting intron retention from RNA-Seq experiments
 
|-
 
|-
−
|[http://staden.sourceforge.net/ io_lib]
+
|[https://github.com/PacificBiosciences/IsoSeq isoseq3]
−
|1.13.10
+
|3.7.0-0
−
|A fully developed set of DNA sequence assembly (Gap4 and Gap5), editing and analysis tools (Spin) for Unix, Linux, MacOSX and MS Windows.
+
|IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application.  
 
|-
 
|-
−
|[http://code.google.com/p/interproscan/ iprscan]
+
|[https://microbiology.se/software/itsx/ ITSx]
−
|4.8-45, 5.2-44, 5.2-45, 5.4-47, 5.7-48, iprscan-5.10-50
+
|1.1.1-IGB-gcc-4.9.4
−
|InterProScan is a bioinformatics tool that provides a one-stop-shop for automated sequence analysis of both protein and nucleic acid, the latter via a full six-frame translation. It offers the ability to identify both structural and functional regions of interest, based upon methods and models that have been generated by a large number of member groups ('member databases').
+
|TSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
 
|-
 
|-
−
|[https://github.com/sequencing isaac-aligner]
+
|[https://github.com/andersen-lab/ivar ivar]
−
|01.14.04.17, 01.14.11.07
+
|1.3.1-IGB-gcc-8.2.0
−
|Isaac: Ultra-fast whole genome secondary analysis on Illumina sequencing platform
+
|iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.
 
|-
 
|-
−
|[https://github.com/sequencing isaac-variantcaller]
+
|[http://www.jalview.org/ Jalview]
−
|1.0.6
+
|2.11.0-Java-1.8.0_152
−
|Isaac: Ultra-fast whole genome secondary analysis on Illumina sequencing platform
+
|
 
|-
 
|-
−
|[http://microbiology.se/software/itsx/ ITSx]
+
|jansson
−
|1.0.11
+
|
−
|ITSx is an open source software utility to extract the highly variable ITS1 and ITS2 subregions from ITS sequences, which is commonly used as a molecular barcode for e.g. fungi. As the inclusion of parts of the neighbouring, very conserved, ribosomal genes (SSU, 5S and LSU rRNA sequences) in the sequence identification process can lead to severely misleading results, ITSx identifies and extracts only the ITS regions themselves.
+
|Jansson is a C library for encoding, decoding and manipulating JSON data.  
 
|-
 
|-
−
|[http://mcmc-jags.sourceforge.net/ JAGS]
+
|[https://github.com/mkirsche/Jasmine Jasmine]
−
|3.4.0
+
|1.1.5
−
|JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation  not wholly unlike BUGS. JAGS was written with three aims in mind:
+
|This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values.  
 
|-
 
|-
−
|[https://www.java.com/ java-32]
+
|[http://www.ece.uvic.ca/~frodo/jasper/ JasPer]
−
|1.7.0_71
+
|1.900.1-IGB-gcc-4.9.4<br>2.0.10-IGB-gcc-4.9.4<br>2.0.14-IGB-gcc-8.2.0
−
|Java is a programming language and computing platform first released by Sun Microsystems in 1995. There are lots of applications and websites that will not work unless you have Java installed, and more are created every day. Java is fast, secure, and reliable. From laptops to datacenters, game consoles to scientific supercomputers, cell phones to the Internet, Java is everywhere!
+
|The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
 
|-
 
|-
−
|[https://www.java.com/ java]
+
|[http://java.com/ Java]
−
|1.6.0_41, 1.7.0_07, 1.7.0_21, 1.7.0_55, 1.8.0_25, 1.8.0_65, 1.8.0_121
+
|1.8.0_121<br>1.8.0_152<br>1.8.0_201<br>11.0.5<br>15.0.1<br>17.0.6
−
|Java is a programming language and computing platform first released by Sun Microsystems in 1995. There are lots of applications and websites that will not work unless you have Java installed, and more are created every day. Java is fast, secure, and reliable. From laptops to datacenters, game consoles to scientific supercomputers, cell phones to the Internet, Java is everywhere!
+
|Java Platform, Standard Edition (Java SE) lets you develop and deployJava applications on desktops and servers.
 
|-
 
|-
−
|[http://www.genome.umd.edu/jellyfish.html jellyfish]
+
|[https://openjfx.io/ JavaFX]
−
|1.1.6, 1.1.11, 2.2.6
+
|21
−
|Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers quickly by using an efficient encoding of a hash table and by exploiting the 'compare-and-swap' CPU instruction to increase parallelism.
+
|JavaFX is an open source, next generation client application platform for desktop, mobile and embedded systems built on Java.  
 
|-
 
|-
−
|[http://www.canonware.com/jemalloc/index.html jemalloc]
+
|[https://github.com/ElArkk/jax-unirep jax-unirep]
−
|4.0.4
+
|0.9-IGB-gcc-4.9.4-Python-3.6.1
 +
|Reimplementation of the UniRep protein featurization model in JAX.
 +
|-
 +
|[http://www.genome.umd.edu/jellyfish.html Jellyfish]
 +
|1.1.12-IGB-gcc-4.9.4<br>1.1.12-IGB-gcc-8.2.0<br>2.2.10-IGB-gcc-8.2.0<br>2.2.6-IGB-gcc-4.9.4<br>2.3.0-IGB-gcc-8.2.0
 +
|Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence.
 +
|-
 +
|jemalloc
 +
|
 
|jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
 
|jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
 
|-
 
|-
−
|[https://pachterlab.github.io/kallisto/ kallisto]
+
|JsonCpp
−
|0.42.4
+
|
−
|kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
+
|JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
 +
|-
 +
|[https://github.com/aidenlab/Juicebox Juicebox]
 +
|1.11.08-Java-1.8.0_201
 +
|Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web
 +
|-
 +
|[https://github.com/aidenlab/juicer Juicer]
 +
|1.6.0-IGB-gcc-8.2.0
 +
|Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps.
 +
|-
 +
|[https://github.com/aidenlab/juicer juicer_tools]
 +
|1.22.01-Java-1.8.0_201
 +
|
 +
|-
 +
|JUnit
 +
|
 +
|A programmer-oriented testing framework for Java.
 +
|-
 +
|[http://jupyter.org/ jupyter]
 +
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
 +
|Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages.
 +
|-
 +
|[http://jupyter.org/ jupyterlab]
 +
|2.2.9-IGB-gcc-8.2.0-Python-3.7.2<br>3.5.0-IGB-gcc-8.2.0-Python-3.10.1
 +
|Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages.
 +
|-
 +
|[http://pachterlab.github.io/kallisto/ kallisto]
 +
|0.43.1-IGB-gcc-4.9.4<br>0.44.0-IGB-gcc-4.9.4
 +
|kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
 +
|-
 +
|[https://github.com/TGAC/KAT KAT]
 +
|2.4.1-IGB-gcc-4.9.4
 +
|KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts.
 +
|-
 +
|[http://genome.cse.ucsc.edu kentUtils]
 +
|353-IGB-gcc-4.9.4
 +
|UCSC genome browser kent bioinformatic utilities
 +
|-
 +
|[https://github.com/fchollet/keras Keras]
 +
|2.0.6-IGB-gcc-4.9.4-Python-2.7.13<br>2.0.8-IGB-gcc-4.9.4-Python-3.6.1<br>2.1.2-IGB-gcc-4.9.4-Python-3.6.1<br>2.1.5-IGB-gcc-4.9.4-Python-3.6.1<br>2.11.0-IGB-gcc-8.2.0-Python-3.7.2<br>2.2.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.2.2-IGB-gcc-4.9.4-Python-3.6.1<br>2.2.4-IGB-gcc-4.9.4-Python-3.6.1<br>2.3.1-IGB-gcc-4.9.4-Python-3.6.1<br>2.3.1-IGB-gcc-4.9.4-Python-3.6.1-TF-2.0.3
 +
|Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.
 +
|-
 +
|[https://github.com/matthiasplappert/keras-rl keras-rl]
 +
|0.3.0-IGB-gcc-4.9.4-Python-2.7.13
 +
|keras-rl implements some state-of-the art deep reinforcement learning algorithms in Python and seamlessly integrates with the deep learning library Keras.
 +
|-
 +
|[https://www.kingrelatedness.com KING]
 +
|2.3.2-IGB-gcc-8.2.0
 +
|KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc.
 +
|-
 +
|[https://bitbucket.org/genomicepidemiology/kma kma]
 +
|1.3.24-IGB-gcc-8.2.0
 +
|KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
 +
|-
 +
|[https://github.com/refresh-bio/KMC KMC]
 +
|3.1.1<br>3.2.1
 +
|KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. The homepage of the KMC project is http://sun.aei.polsl.pl/kmc
 +
|-
 +
|[https://github.com/fanagislab/kmerfreq kmerfreq]
 +
|4.0-IGB-gcc-8.2.0
 +
|kmerfreq count K-mer (with size K) frequency from the input sequence data, typically sequencing reads data, and reference genome data is also applicable.
 +
|-
 +
|[https://bitbucket.org/biobakery/kneaddata/wiki/Home KneadData]
 +
|0.10.0-IGB-gcc-8.2.0-Python-3.7.2<br>0.12.0-IGB-gcc-8.2.0-Python-3.7.2<br>0.6.1-IGB-gcc-4.9.4-Python-3.6.1<br>0.8.0-IGB-gcc-8.2.0-Python-3.7.2
 +
|KneadData is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the host. However, metagenomic sequencing data from such experiments will often contain a high ratio of host to bacterial reads. This tool aims to perform principled in silico separation of bacterial reads from these contaminant reads, be they from the host, from bacterial 16S sequences, or other user-defined sources.
 +
|-
 +
|[https://ccb.jhu.edu/software/kraken/ Kraken]
 +
|1.0-IGB-gcc-4.9.4<br>1.1.1-IGB-gcc-8.2.0
 +
|Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs.
 +
|-
 +
|[https://ccb.jhu.edu/software/kraken/ Kraken2]
 +
|2.0.8-beta-IGB-gcc-4.9.4<br>2.1.1-IGB-gcc-8.2.0<br>2.1.2-IGB-gcc-8.2.0
 +
|Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs.
 +
|-
 +
|[https://github.com/jenniferlu717/KrakenTools KrakenTools]
 +
|1.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results.
 +
|-
 +
|[https://github.com/marbl/Krona Krona]
 +
|2.7-IGB-gcc-4.9.4-Perl-5.24.1
 +
|Interactively explore metagenomes and more from a web browser.
 +
|-
 +
|[https://github.com/alticelabs/kyoto kyoto]
 +
|20170410-IGB-gcc-4.9.4
 +
|Kyoto Tycoon is a lightweight network server on top of the Kyoto Cabinet key-value database, built for high-performance and concurrency. Some of its features include:
 +
|-
 +
|[http://lame.sourceforge.net/ LAME]
 +
|3.99.5-IGB-gcc-4.9.4
 +
|LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
 +
|-
 +
|[http://lasagne.readthedocs.io/en/latest/index.html Lasagne]
 +
|20170606-IGB-gcc-4.9.4-Python-2.7.13
 +
|Lasagne is a lightweight library to build and train neural networks in Theano. - Homepage: http://lasagne.readthedocs.io/en/latest/index.html
 +
|-
 +
|[https://gitlab.com/mcfrith/last/ last]
 +
|1257-IGB-gcc-8.2.0
 +
|LAST is designed for moderately large data (e.g. genomes, DNA reads,proteomes).
 +
|-
 +
|[http://www.bx.psu.edu/~rsharris/lastz/ LASTZ]
 +
|1.04.00-IGB-gcc-4.9.4
 +
|LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS  sequencing technologies such as Roche 454. - Homepage: http://www.bx.psu.edu/~rsharris/lastz/
 +
|-
 +
|[http://lbzip2.org/ lbzip2]
 +
|2.5-IGB-gcc-4.9.4
 +
|lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format.
 +
|-
 +
|[https://bitbucket.org/nsegata/lefse LEfSe]
 +
|20180219-IGB-gcc-4.9.4-Python-2.7.13
 +
|LEfSe
 +
|-
 +
|[https://sourceforge.net/p/lep-map3/wiki/LM3%20Home/ Lep-MAP3]
 +
|20221128-Java-15.0.1
 +
|Lep-MAP3 (LM3) is a novel linkage map construction software suite. It can handle millions of markers and thousands of individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them.
 +
|-
 +
|[https://lftp.yar.ru/ lftp]
 +
|4.9.2-IGB-gcc-8.2.0
 +
|FTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).  
 
|-
 
|-
−
|[https://github.com/ged-lab/khmer khmer]
+
|[https://gitlab.dkrz.de/k202009/libaec libaec]
−
|1.3, 2.0
+
|1.0.6-IGB-gcc-8.2.0
−
|khmer is a library and suite of command line tools for working with DNA sequence. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform. khmer takes a k-mer-centric approach to sequence analysis, hence the name.
+
|Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers(samples). The library achieves best results for low entropy data as often encountered in space imaginginstrument data or numerical model output from weather or climate simulations. While floating point representationsare not directly supported, they can also be efficiently coded by grouping exponents and mantissa.
 
|-
 
|-
−
|[http://kmergenie.bx.psu.edu/ kmergenie]
+
|libBigWig
−
|1.5854, 1.6950
+
|
−
|KmerGenie estimates the best k-mer length for genome de novo assembly. Given a set of reads, KmerGenie first computes the k-mer abundance histogram for many values of k. Then, for each value of k, it predicts the number of distinct genomic k-mers in the dataset, and returns the k-mer length which maximizes this number. Experiments show that KmerGenie's choices lead to assemblies that are close to the best possible over all k-mer lengths.
+
|A C library for reading/parsing local and remote bigWig and bigBed files. While Kent's source code is free to use for these purposes
 
|-
 
|-
−
|[https://ccb.jhu.edu/software/kraken/ kraken]
+
|libcerf
−
|0.10.5b
+
|
−
|Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
+
|libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.
 
|-
 
|-
−
|[https://github.com/SchulzLab/KREATION KREATION]
+
|libdap
−
|20170214
+
|
−
|KREATION calculates the contribution of each assembly.
+
|A C++ SDK which contains an implementation of DAP 2.0 and the development versions of DAP3, up to 3.4. This includes both Client- and Server-side support classes.
 
|-
 
|-
−
|[http://sourceforge.net/projects/krona/ krona]
+
|libdrm
−
|2.2
+
|
−
|Krona allows hierarchical data to be explored with zoomable HTML5 pie charts. Krona charts can be created using an Excel template or Krona Tools, which includes support for several bioinformatics tools and raw data formats.
+
|Direct Rendering Manager runtime library.
 
|-
 
|-
−
|[http://evolution.genetics.washington.edu/lamarc/index.html lamarc]
+
|libevent
−
|2.1.8
+
|
−
|LAMARC is a program which estimates population-genetic parameters such as population size, population growth rate, recombination rate, and migration rates. It approximates a summation over all possible genealogies that could explain the observed sample, which may be sequence, SNP, microsatellite, or electrophoretic data. LAMARC and its sister program Migrate are successor programs to the older programs Coalesce, Fluctuate, and Recombine, which are no longer being supported. The programs are memory-intensive but can run effectively on workstations; we support a variety of operating systems.
+
|The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
 
|-
 
|-
−
|[http://www.netlib.org/lapack/ lapack]
+
|libfaketime
−
|3.5.0, 3.6.0
+
|
−
|LAPACK is written in Fortran 90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. The associated matrix factorizations (LU, Cholesky, QR, SVD, Schur, generalized Schur) are also provided, as are related computations such as reordering of the Schur factorizations and estimating condition numbers. Dense and banded matrices are handled, but not general sparse matrices. In all areas, similar functionality is provided for real and complex matrices, in both single and double precision.
+
|libfaketime intercepts various system calls that programs use to retrieve thecurrent date and time. It then reports modified (faked) dates and times (asspecified by you, the user) to these programs. This means you can modify thesystem time a program sees without having to change the time system-wide.
 
|-
 
|-
−
|[http://last.cbrc.jp/ last]
+
|libffi
−
|278, 545
+
|
−
|Finds similar regions between sequences.
+
|The libffi library provides a portable, high level programming interface to various callingconventions. This allows a programmer to call any function specified by a call interface description at run-time.
 
|-
 
|-
−
|[http://www.bx.psu.edu/~rsharris/lastz/ lastz]
+
|libgd
−
|1.02.00
+
|
−
|LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454.
+
|GD is an open source code library for the dynamic creation of images by programmers.
 
|-
 
|-
−
|[http://bioinformatics.ninja/libcrispr/ libcrispr]
+
|libgdiplus
−
|1.0.1
+
|
−
|A .crispr file is an opensource XML markup for describing clustered regularly interspersed short palindromic repeats (CRISPR). This includes information about the repeats, spacers and their arrangement.
+
|An Open Source implementation of the GDI+ API
 +
|-
 +
|libglvnd
 +
|
 +
|libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
 +
|-
 +
|[http://deeplearning.net/software/libgpuarray/ libgpuarray]
 +
|0.6.5-IGB-gcc-4.9.4
 +
|Make a common GPU ndarray(n dimensions array) that can be reused by all projects that is as future proof as possible, while keeping it easy to use for simple need/quick test. - Homepage: http://deeplearning.net/software/libgpuarray/
 +
|-
 +
|libgtextutils
 +
|
 +
|ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream - Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
 +
|-
 +
|libharu
 +
|
 +
|libHaru is a free, cross platform, open source library for generating PDF files.
 +
|-
 +
|libjpeg-turbo
 +
|
 +
|libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEGcompression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
 +
|-
 +
|libpciaccess
 +
|
 +
|Generic PCI access library.
 +
|-
 +
|libpng
 +
|
 +
|libpng is the official PNG reference library
 +
|-
 +
|libpthread-stubs
 +
|
 +
|The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint,latency hiding, direct access to the protocol, improved threading support, and extensibility.
 +
|-
 +
|libreadline
 +
|
 +
|The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
 +
|-
 +
|libsodium
 +
|
 +
|Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
 +
|-
 +
|[https://www.csie.ntu.edu.tw/~cjlin/libsvm/ libsvm]
 +
|3.24-IGB-gcc-4.9.4
 +
|LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.
 +
|-
 +
|LibTIFF
 +
|
 +
|tiff: Library and tools for reading and writing TIFF data files
 +
|-
 +
|libtool
 +
|
 +
|GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. - Homepage: http://www.gnu.org/software/libtool
 +
|-
 +
|[https://www.nongnu.org/libunwind/ libunwind]
 +
|1.3.1-IGB-gcc-4.9.4<br>1.5.0-IGB-gcc-8.2.0
 +
|The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
 +
|-
 +
|LibUUID
 +
|
 +
|Portable uuid C library
 +
|-
 +
|libXft
 +
|
 +
|X11 client-side library
 +
|-
 +
|libxml2
 +
|
 +
|Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
 +
|-
 +
|libxslt
 +
|
 +
|Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
 
|-
 
|-
−
|[http://sbml.org/Main_Page libsbml]
+
|[https://github.com/agshumate/Liftoff Liftoff]
−
|5.12.1
+
|1.6.1-IGB-gcc-8.2.0-Python-3.7.2
−
|Systems Biology Markup Language (SBML), a free and open interchange format for computer models of biological processes.
+
|Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.
 
|-
 
|-
−
|[http://fun.bio.keio.ac.jp/software/libsbmlsim/ libsbmlsim]
+
|[https://lima.how/ lima]
−
|1.1.0
+
|2.6.0-0
−
|LibSBMLSim is a library for simulating an SBML model which contains Ordinary Differential Equations (ODEs). LibSBMLSim provides simple command-line tool and several APIs to load an SBML model, perform numerical integration (simulate) and export its results. Both explicit and implicit methods are supported on libSBMLSim.
+
|lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data. It powers the Demultiplex Barcodes, Iso-Seq, and Mark PCR Duplicates GUI-based analysis applications.
 
|-
 
|-
−
|[http://www.icir.org/christian/libstree/ libstree]
+
|[http://www.bcgsc.ca/platform/bioinfo/software/links LINKS]
−
|0.4.2
+
|1.8.5-IGB-gcc-4.9.4-Perl-5.24.1<br>1.8.7-IGB-gcc-4.9.4-Perl-5.24.1<br>1.8.7-IGB-gcc-8.2.0-Perl-5.28.1
−
|libstree is a generic suffix tree implementation, written in C. It can handle arbitrary data structures as elements of a string. Unlike most demo implementations, it is not limited to simple ASCII character strings.
+
|LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences. It provides a generic alignment-free framework for scaffolding and can work on any sequences. It is versatile and supports not only long sequences as a source of long-range information, but also MPET pairs and linked-reads, such as those from the 10X Genomics GemCode and Chromium platform, via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer).
 
|-
 
|-
−
|[http://xmlsoft.org/ libxml2]
+
|LittleCMS
−
|2.9.1
+
|
−
|Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License.
+
|Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.  - Homepage: http://www.littlecms.com/
 
|-
 
|-
−
|[http://xmlsoft.org/libxslt/index.html libxslt]
+
|[http://llvm.org/ LLVM]
−
|1.1.28
+
|10.0.1-IGB-gcc-8.2.0<br>4.0.1-IGB-gcc-4.9.4<br>6.0.0-IGB-gcc-4.9.4
−
|Libxslt is the XSLT C library developed for the GNOME project. XSLT itself is a an XML language to define transformation for XML.
+
|The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
 
|-
 
|-
−
|[http://llvm.org/ llvm]
+
|[https://symas.com/lmdb LMDB]
−
|4.0.0
+
|0.9.22-IGB-gcc-4.9.4
−
|The LLVM Project is a collection of modular and reusable compiler and toolchain technologies.
+
|LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.
 
|-
 
|-
−
|[http://melissagymrek.com/lobstr-code/index.html lobSTR]
+
|[https://csb5.github.io/lofreq/ lofreq]
−
|3.0.3
+
|2.1.5-IGB-gcc-4.9.4-Python-2.7.13
−
|lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.
+
|:oFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.
 
|-
 
|-
 
|[http://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger longranger]
 
|[http://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger longranger]
−
|2.1.0, 2.1.2
+
|2.1.3<br>2.1.6<br>2.2.2
 
|Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. There are five main pipelines, each triggered by a longranger command
 
|Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. There are five main pipelines, each triggered by a longranger command
 
|-
 
|-
−
|[http://support.10xgenomics.com/genome-exome/software/visualization/latest/what-is-loupe loupe]
+
|[https://github.com/LappalainenLab/lorals lorals]
−
|2.1.0
+
|20210528-IGB-gcc-8.2.0-Python-3.7.2
−
|Loupe is a genome browser designed to visualize the Linked-Read data produced by the 10x Chromium Platform. Loupe is named for a jeweler's loupe, which is used to inspect gems.
+
|A Python package for allele-specific analyses in long-read data.
 +
|-
 +
|[https://github.com/bcm-uga/Loter Loter]
 +
|20210413-IGB-gcc-8.2.0-Python-3.7.2
 +
|Loter is a Python (and soon R) package for local ancestry inference [1] and haplotype phasing [2]
 +
|-
 +
|[https://support.10xgenomics.com/genome-exome/software/visualization/latest/what-is-loupe loupe]
 +
|2.1.1
 +
|Loupe is a genome browser designed to visualize the Linked-Read data produced by the 10x Chromium Platform. Loupe is named for a jewelers loupe, which is used to inspect gems.
 +
|-
 +
|[https://sourceforge.net/projects/lpsolve/ lpsolve]
 +
|5.5.2.5-IGB-gcc-4.9.4<br>5.5.2.5-IGB-gcc-8.2.0
 +
|Mixed Integer Linear Programming (MILP) solver
 
|-
 
|-
−
|[http://lpsolve.sourceforge.net/ lp_solve]
+
|[https://github.com/anuradhawick/LRBinner LRBinner]
−
|5.5.2
+
|0.1-IGB-gcc-8.2.0-Python-3.7.2
−
|lp_solve is a free (see LGPL for the GNU lesser general public license) linear (integer) programming solver based on the revised simplex method and the Branch-and-bound method for the integers.
+
|Binning Error-Prone Long Reads Using Auto Encoders
 
|-
 
|-
−
|[http://komarix.org/ac/lr/ LR-TRIRLS]
+
|[https://github.com/oushujun/LTR_retriever LTRretriever]
−
|20060531
+
|2.9.0-IGB-gcc-4.9.4-Perl-5.24.1
−
|LR-TRIRLS stands for Logistic Regression with Truncated Regularized Iteratively Re-weighted Least Squares. This is our contribution to LR computation.
+
|LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and generates non-redundant LTR-RT library for genome annotations.
 
|-
 
|-
−
|[http://www.lua.org/ lua]
+
|[http://www.lua.org/ Lua]
−
|5.1.4, 5.2.2
+
|5.1.5-IGB-gcc-4.9.4<br>5.1.5-IGB-gcc-8.2.0<br>5.3.4-IGB-gcc-4.9.4
 
|Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
 
|Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
 
|-
 
|-
 
|[https://github.com/arq5x/lumpy-sv lumpy-sv]
 
|[https://github.com/arq5x/lumpy-sv lumpy-sv]
−
|0.2.13
+
|0.3.0-IGB-gcc-4.9.4
 
|A probabilistic framework for structural variant discovery.
 
|A probabilistic framework for structural variant discovery.
 +
|-
 +
|[https://lz4.github.io/lz4/ lz4]
 +
|1.9.2-IGB-gcc-4.9.4<br>1.9.2-IGB-gcc-8.2.0
 +
|LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core.  It features an extremely fast decoder, with speed in multiple GB/s per core.
 +
|-
 +
|lzo
 +
|
 +
|Portable lossless data compression library
 +
|-
 +
|M4
 +
|
 +
|GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions  (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. - Homepage: http://www.gnu.org/software/m4/m4.html
 
|-
 
|-
 
|[http://liulab.dfci.harvard.edu/MACS/ MACS]
 
|[http://liulab.dfci.harvard.edu/MACS/ MACS]
−
|1.4.2, 1.4.2-1, 2.0.10, 2.1.0
+
|1.4.2-1-IGB-gcc-4.9.4-Python-2.7.13
−
|Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites.
+
|Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture  local biases in the genome sequence, allowing for more sensitive and robust prediction.
 
|-
 
|-
−
|[http://mafft.cbrc.jp/alignment/software/ mafft]
+
|[https://github.com/taoliu/MACS/ MACS2]
−
|6.953, 7.130
+
|2.1.1.20160309-IGB-gcc-4.9.4-Python-2.7.13<br>2.1.2-IGB-gcc-4.9.4-Python-2.7.13<br>2.2.5-IGB-gcc-4.9.4-Python-3.6.1<br>2.2.5-IGB-gcc-8.2.0-Python-3.7.2
−
|MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼30,000 sequences), etc.
+
|Model Based Analysis for ChIP-Seq data
 
|-
 
|-
−
|[http://www.yandell-lab.org/software/maker.html maker]
+
|[http://mafft.cbrc.jp/alignment/software/ MAFFT]
−
|2.31.9
+
|7.310-IGB-gcc-4.9.4<br>7.490-IGB-gcc-8.2.0
−
|MAKER is a portable and easily configurable genome annotation pipeline.
+
|MAFFT is a multiple sequence alignment program  for unix-like operating systems.  It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences),  FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.
 
|-
 
|-
−
|[https://mariadb.org/ mariadb]
+
|[https://bitbucket.org/liulab/mageck-vispr mageck-vispr]
−
|10.1.24
+
|0.5.4-IGB-gcc-4.9.4-Python-3.6.1
−
|MariaDB Server is one of the most popular database servers in the world. It’s made by the original developers of MySQL and guaranteed to stay open source. Notable users include Wikipedia, WordPress.com and Google.
+
|MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
 
|-
 
|-
−
|[http://sourceforge.net/projects/metavar/ MaryGold]
+
|[https://github.com/DpeerLab/magic magic]
−
|0.2
+
|0.1-IGB-gcc-4.9.4-Python-3.6.1<br>0.1.1-IGB-gcc-4.9.4-Python-3.6.1
−
|The package enables detection of sequence variation between metagenomic samples.
+
|A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data
 +
|-
 +
|[http://www.yandell-lab.org/software/maker.html MAKER]
 +
|2.31.9-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded<br>3.00.0-beta-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded<br>3.01.03-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded<br>3.01.1-beta-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
 +
|MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKERs inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
 +
|-
 +
|[http://www.makotemplates.org Mako]
 +
|1.0.6-IGB-gcc-4.9.4-Python-3.6.1
 +
|A super-fast templating language that borrows the best ideas from the existing templating languages
 +
|-
 +
|[https://github.com/Illumina/manta manta]
 +
|1.6.0-IGB-gcc-8.2.0
 +
|Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
 +
|-
 +
|[https://github.com/ginolhac/mapDamage mapDamage]
 +
|2.0.5-IGB-gcc-4.9.4-Python-2.7.13<br>2.0.9-IGB-gcc-4.9.4-Python-2.7.13
 +
|mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
 +
|-
 +
|[https://github.com/LynchLab/MAPGD MAPGD]
 +
|0.4.26-IGB-gcc-4.9.4
 +
|MAPGD is a series of related programs that estimate allele frequency, heterozygosity, Hardy-Weinberg disequilibrium, linkage disequilibrium and identity-by-descent (IBD) coefficients from population genomic data using a statistically rigorous maximum likelihood approach.
 +
|-
 +
|[http://www.netlab.uky.edu/p/bioinfo/MapSplice2 MapSplice]
 +
|2.2.1-IGB-gcc-4.9.4-Python-2.7.13
 +
|MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.
 +
|-
 +
|[https://mariadb.org/ MariaDB]
 +
|10.1.31-IGB-gcc-4.9.4<br>10.1.31-IGB-gcc-8.2.0<br>10.3.17-IGB-gcc-8.2.0<br>5.5.58-IGB-gcc-4.9.4
 +
|MariaDB An enhanced, drop-in replacement for MySQL.
 +
|-
 +
|[https://github.com/marbl/Mash Mash]
 +
|2.2.2-IGB-gcc-8.2.0
 +
|Fast genome and metagenome distance estimation using MinHash
 +
|-
 +
|[https://github.com/marbl/MashMap MashMap]
 +
|2.0
 +
|MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s).
 +
|-
 +
|[https://github.com/matterport/Mask_RCNN MaskRCNN]
 +
|20190227-IGB-gcc-4.9.4-Python-3.6.1
 +
|This is an implementation of Mask R-CNN on Python 3, Keras, and TensorFlow. The model generates bounding boxes and segmentation masks for each instance of an object in the image.  
 
|-
 
|-
 
|[http://www.genome.umd.edu/masurca.html MaSuRCA]
 
|[http://www.genome.umd.edu/masurca.html MaSuRCA]
−
|3.2.2_RC1
+
|3.2.3-IGB-gcc-4.9.4<br>3.4.2-IGB-gcc-8.2.0<br>4.0.5-IGB-gcc-8.2.0
−
|MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches
+
|MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph   and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing  only short reads from Illumina sequencing or a mixture of short reads and long reads  (Sanger, 454, Pacbio and Nanopore).
 
|-
 
|-
−
|[http://www.mathworks.com/products/matlab/ matlab]
+
|[http://www.mathworks.com/products/matlab MATLAB]
−
|r2010b, r2013a, r2013b, r2014b
+
|2017a<br>2017b<br>2020b-IGB-gcc-8.2.0
−
|MATLAB® is a high-level language and interactive environment for numerical computation, visualization, and programming. Using MATLAB, you can analyze data, develop algorithms, and create models and applications.
+
|MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
 
|-
 
|-
−
|[http://gel.ahabs.wisc.edu/mauve/download.php mauve]
+
|[https://www.mathworks.com/help/matlab/matlab-engine-for-python.html MATLAB-python]
−
|2.3.1
+
|2017b-IGB-gcc-4.9.4-Python-3.6.1<br>2020b-IGB-gcc-8.2.0-Python-3.7.2
−
|Mauve is a system for efficiently constructing multiple genome alignments in the presence of large-scale evolutionary events such as rearrangement and inversion. Multiple genome alignment provides a basis for research into comparative genomics and the study of evolutionary dynamics. Aligning whole genomes is a fundamentally different problem than aligning short sequences.
+
|The MATLAB Engine API for Python provides a package for Python to call MATLAB as a computational engine. The engine supports the reference implementation (CPython) for Python versions 2.7, 3.5, and 3.6.
 
|-
 
|-
−
|[http://sourceforge.net/projects/maxbin2/ MaxBin]
+
|[https://invisible-island.net/mawk/ mawk]
−
|2.0.1
+
|1.3.4-20200120-IGB-gcc-8.2.0
−
|MaxBin2 is the next-generation of MaxBin (https://sourceforge.net/projects/maxbin/) that supports multiple samples at the same time. MaxBin is a software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm.
+
|mawk is an interpreter for the AWK Programming Language.
 
|-
 
|-
−
|[http://datadryad.org/resource/doi:10.5061/dryad.r9k57.2 maxcutpack]
+
|[https://sourceforge.net/projects/maxbin2 maxbin2]
−
|3.0
+
|2.2.7-IGB-gcc-4.9.4
−
|The software generates a phylogenic tree using the Weighted Quartet MaxCut Algorithm
+
|MaxBin2 is the next-generation of MaxBin (https://sourceforge.net/projects/maxbin/) that supports multiple samples at the same time.
 
|-
 
|-
−
|[http://www.multicorewareinc.com/bioinformatics/ mblast]
+
|[http://www.coxdocs.org/doku.php?id=maxquant:start MaxQuant]
−
|1.4.2
+
|1.6.15.0-IGB-gcc-4.9.4<br>1.6.7.0-IGB-gcc-4.9.4
−
|MulticoreWare Inc. has implemented the BLAST algorithm with a parallelized, performance-optimized design. This parallelized implementation is called mBLAST.
+
|MaxQuant is a proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.  
 
|-
 
|-
−
|[http://micans.org/mcl/index.html mcl]
+
|[https://github.com/mcveanlab/mccortex McCortex]
−
|12-068
+
|1.0.1-IGB-gcc-4.9.4
−
|The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs.
+
|Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and without a reference genome. Between closely related samples or highly diverged ones. From bacterial to mammalian genomes. Minimal configuration. And it's free.
 +
|-
 +
|[http://micans.org/mcl/ MCL]
 +
|14.137-IGB-gcc-4.9.4<br>14.137-IGB-gcc-8.2.0
 +
|The MCL algorithm is short for the Markov Cluster Algorithm, a fastand scalable unsupervised cluster algorithm for graphs (also known as networks) basedon simulation of (stochastic) flow in graphs.  
 +
|-
 +
|MCScanX
 +
|20221031-IGB-gcc-8.2.0
 +
|
 
|-
 
|-
−
|[http://www.mathworks.com/products/compiler/mcr/ MCR]
+
|[https://github.com/nanoporetech/medaka medaka]
−
|r2013a
+
|0.1.0-IGB-gcc-4.9.4-Python-3.6.1
−
|The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
+
|Medaka demonstrates a framework for error correcting sequencing data, particularly aimed at nanopore sequencing. Tools are provided for both training and inference. The code exploits the keras deep learning library.
 
|-
 
|-
−
|[https://github.com/voutcn/megahit megahit]
+
|[https://github.com/voutcn/megahit MEGAHIT]
−
|0.2.1
+
|1.1.1-IGB-gcc-4.9.4<br>1.2.9-IGB-gcc-8.2.0
 
|MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly.
 
|MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly.
 
|-
 
|-
−
|[http://ab.inf.uni-tuebingen.de/software/megan/ MEGAN]
+
|[https://github.com/nanoporetech/megalodon/ megalodon]
−
|4.70.4, 5.1.0
+
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.0.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.1.1-IGB-gcc-8.2.0-Python-3.7.2<br>2.2.0-IGB-gcc-8.2.0-Python-3.7.2<br>2.2.4-IGB-gcc-8.2.0-Python-3.7.2<br>2.3.4-IGB-gcc-8.2.0-Python-3.7.2
−
|In metagenomics, the aim is to understand the composition and operation of complex microbial consortia in environmental samples through sequencing and analysis of their DNA. Similarly, metatranscriptomics and metaproteomics target the RNA and proteins obtained from such samples.
+
|Megalodon is a research tool for per-read and aggregated modified base and sequence variant calling by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
 +
|-
 +
|[http://ab.inf.uni-tuebingen.de/software/megan6/ MEGAN]
 +
|6.12.2-Java-1.8.0_152
 +
|MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.
 +
|-
 +
|[http://meme-suite.org/ MEME]
 +
|4.11.2-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13<br>4.12.0-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13<br>5.0.1-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13<br>5.0.5-IGB-gcc-4.9.4<br>5.5.1-IGB-gcc-8.2.0
 +
|The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or  GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using  MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate  motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment  using SpaMo or CentriMo.
 +
|-
 +
|[https://github.com/IGBIllinois/memprof memprof]
 +
|1.01
 +
|Memprof is HPC Cluster Program Profiler. It records the memory, processor, and IO usage of a process. It will then generate a graph of the results.
 +
|-
 +
|[https://sourceforge.net/projects/meraculous20/ Meraculous-2d]
 +
|2.2.6-IGB-gcc-4.9.4
 +
|Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements.
 +
|-
 +
|[https://github.com/arangrhie/merfin Merfin]
 +
|1.1-IGB-gcc-8.2.0<br>20210507-IGB-gcc-8.2.0
 +
|k-mer-based assembly and variant calling evaluation for improved consensus accuracy.
 +
|-
 +
|[https://github.com/Roy-lab/merlin-p merlin-p]
 +
|20181020-IGB-gcc-8.2.0
 +
|Modular regulatory network learning with per gene information (MERLIN) is a network inference method that tries to infer a more accurate regulatory network by incorporating a modularity constraint.
 +
|-
 +
|[https://github.com/marbl/merqury merqury]
 +
|1.3-IGB-gcc-8.2.0
 +
|Evaluate genome assemblies with k-mers and more
 +
|-
 +
|meryl
 +
|1.3
 +
|
 +
|-
 +
|[https://www.mesa3d.org/ Mesa]
 +
|20.0.2-IGB-gcc-4.9.4
 +
|Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
 
|-
 
|-
−
|[http://meme.nbcr.net/meme/ meme]
+
|[https://mesonbuild.com Meson]
−
|4.10.0-1, 4.11.4_1
+
|0.51.2-IGB-gcc-4.9.4-Python-3.6.1
−
|Motif-based sequence analysis tools
+
|Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
 
|-
 
|-
−
|[https://bitbucket.org/berkeleylab/metabat metabat]
+
|[https://bitbucket.org/berkeleylab/metabat MetaBAT]
−
|0.26.1
+
|2.12.1<br>2.15-IGB-gcc-8.2.0
−
|MetaBAT, An Efficient Tool for Accurately Reconstructing Single Genomes from Complex Microbial Communities
+
|MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
 
|-
 
|-
−
|metageneannotator
+
|[https://github.com/soedinglab/metaeuk MetaEuk]
−
|1.0
+
|4-IGB-gcc-8.2.0
 +
|MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to recover optimal exons sets.
 +
|-
 +
|[http://metagene.nig.ac.jp/ MetaGeneAnnotator]
 +
|20080819-x86-64
 
|MetaGeneAnnotator is a gene-finding program for prokaryote and phage.
 
|MetaGeneAnnotator is a gene-finding program for prokaryote and phage.
 
|-
 
|-
−
|[http://exon.gatech.edu/meta_gmhmmp.cgi MetaGeneMark]
+
|[https://github.com/gatech-genemark/MetaGeneMark-2 MetaGeneMark-2]
−
|2010
+
|20210406-IGB-gcc-8.2.0
−
|Gene Prediction in Bacteria, Archaea, Metagenomes and Metatranscriptomes
+
|MetaGeneMark-2 is an unsupervised metagenomic gene finder. It improves on MetaGeneMark by adding models for better gene start prediction, as well as automatic selection of genetic code (4 or 11).
 +
|-
 +
|[https://github.com/GaetanBenoitDev/metaMDBG metaMDBG]
 +
|0.3
 +
|MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly.
 
|-
 
|-
−
|[http://cbcb.umd.edu/software/metAMOS metAMOS]
+
|[https://github.com/biobakery/MetaPhlAn/tree/3.0 metaphlan]
−
|1.2
+
|3.0.4-IGB-gcc-8.2.0-Python-3.7.2<br>3.0.7-IGB-gcc-8.2.0-Python-3.7.2<br>3.1.0-IGB-gcc-8.2.0-Python-3.7.2<br>4.0.0-IGB-gcc-8.2.0-Python-3.7.2<br>4.0.6-IGB-gcc-8.2.0-Python-3.7.2
−
|metAMOS is an integrated assembly and analysis pipeline for metagenomic data. It is built around the Bambus2 metagenomic scaffolder and includes many current tools for assembly, gene finding, and taxonomic classification.
+
|MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.
 
|-
 
|-
−
|[https://bitbucket.org/nsegata/metaphlan/wiki/Home metaphlan]
+
|[https://bitbucket.org/biobakery/metaphlan2 metaphlan2]
−
|1.7.8
+
|2.6.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.7.6-IGB-gcc-4.9.4-Python-2.7.13<br>2.7.8-IGB-gcc-4.9.4-Python-2.7.13<br>2.7.8-IGB-gcc-4.9.4-Python-3.6.1
−
|MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data. MetaPhlAn relies on unique clade-specific marker genes identified from 3,000 reference genomes
+
|MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
 
|-
 
|-
−
|[https://github.com/snayfach/metatrans metatrans]
+
|[https://www.agisoft.com metashape]
−
|11-4-2014
+
|1.7.1-IGB-gcc-8.2.0<br>2.0.1
−
|Translate metagenomic reads
+
|Agisoft Metashape is a stand-alone software product that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales.
 
|-
 
|-
−
|[http://metavelvet.dna.bio.keio.ac.jp/MSL.html MetaVelvet-SL]
+
|[https://www.agisoft.com metashape-pro]
−
|1.0
+
|1.8.4-IGB-gcc-8.2.0<br>2.0.1<br>2.0.2
−
|MetaVelvet identifies shared nodes (named chimeric nodes) between two subgraphs and disconnects two subgraphs by splitting the shared nodes. To identify chimeric nodes, MetaVelvet uses a simple heuristics based on coverage difference and paired-end information.
+
|Agisoft Metashape is a stand-alone software product that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales.
 +
|-
 +
|[https://www.agisoft.com metashape-python]
 +
|1.7.1-IGB-gcc-8.2.0-Python-3.7.2<br>2.0.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|Process digital images and generate 3D spatial data. Fast and highly accurate.
 +
|-
 +
|[https://metavelvet.dna.bio.keio.ac.jp/ MetaVelvet]
 +
|1.2.02-IGB-gcc-4.9.4
 +
|An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
 +
|-
 +
|[https://github.com/ablab/spades/tree/metaviral_publication metaviralSPAdes]
 +
|20200721-IGB-gcc-8.2.0-Python-3.7.2
 +
|It contains script for viral assembly from metagenomes (assembler/metaviralspades.py), which is based on metaplasmidSPAdes.
 +
|-
 +
|[https://github.com/bxlab/metaWRAP metaWRAP]
 +
|1.2.3<br>1.3.2
 +
|MetaWRAP also includes a novel bin reassembly module, which allows to drastically improve the quality of a set of bins by extracting the reads belonging to each bin, and reassembling the bins with a more permissive, non-metagenomic assembler.
 +
|-
 +
|[http://glaros.dtc.umn.edu/gkhome/metis/metis/overview METIS]
 +
|5.1.0-IGB-gcc-4.9.4
 +
|METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes,and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on themultilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
 
|-
 
|-
−
|[http://metavelvet.dna.bio.keio.ac.jp/ MetaVelvet]
+
|[http://unafold.rna.albany.edu/?q=mfold mfold]
−
|1.2.02, 1.2.02-kmer245
+
|4.7-IGB-gcc-8.2.0
−
|MetaVelvet : An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
+
|The mfold web server is one of the oldest web servers in computational molecular biology.
 
|-
 
|-
−
|[http://wws.weizmann.ac.il/mcb/UriAlon/download/network-motif-software mfinder]
+
|[http://microbiomeutil.sourceforge.net/ microbiomeutil]
−
|1.2
+
|20110519-IGB-gcc-4.9.4
−
|mfinder is a software tool for network motifs detection.
+
|Contains ChimeraSlayer, WigeoN, and NAST-iEr
 
|-
 
|-
−
|[https://github.com/mlangill/microbiome_helper microbiome_helper]
+
|[https://github.com/LangilleLab/microbiome_helper microbiome_helper]
−
|20170217
+
|20171114-IGB-gcc-4.9.4
 
|An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools. We provide workflows, tutorials and a virtual box image to help researchers process microbial data.
 
|An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools. We provide workflows, tutorials and a virtual box image to help researchers process microbial data.
 
|-
 
|-
−
|[http://sourceforge.net/p/mira-assembler/wiki/Home/ mira]
+
|[https://github.com/lh3/miniasm miniasm]
−
|3.2.1, 4.0.2
+
|0.2-IGB-gcc-4.9.4
−
|MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads)
+
|Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.
 
|-
 
|-
−
|[https://www.mdc-berlin.de/8551903/en/ miRDeep]
+
|[https://www.continuum.io/anaconda-overview Miniconda2]
−
|20151029
+
|4.7.12.1
−
|miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades. The low consumption of time and memory combined with user-friendly interactive graphic output makes miRDeep2 accessible for straightforward application in current reasearch.
+
|Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
 
|-
 
|-
−
|[http://vm-lux.embl.de/~kultima/MOCAT/ MOCAT]
+
|[https://www.continuum.io/anaconda-overview Miniconda3]
−
|1.1
+
|23.5.2<br>4.10.3<br>4.7.12.1
−
|MOCAT is a package for analyzing metagenomics datasets. Currently MOCAT supports Illumina single- and paired-end reads in raw FastQ format. Using MOCAT you can, for example, generate taxonomic profiles of, and assemble, metagenomes.
+
|Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
 
|-
 
|-
−
|[https://bitbucket.org/msipos/modalclust ModalClust]
+
|[https://github.com/lh3/minimap minimap]
−
|0.2, 0.3
+
|0.2-IGB-gcc-4.9.4<br>2.11-IGB-gcc-4.9.4<br>2.16-IGB-gcc-4.9.4-Python-3.6.1<br>2.17-IGB-gcc-8.2.0<br>2.18-IGB-gcc-8.2.0<br>2.21-IGB-gcc-8.2.0<br>2.3-IGB-gcc-4.9.4<br>2.8-IGB-gcc-4.9.4
−
|Modal Clust is a program that clusters genomic sequences to 3% similarity. Modal clust was originally a command in R and was modified by Maksim Sipos and Carl Yeoman for use in 454 pyrosequencing data processing.
+
|Minimap is an experimental tool to efficiently find multiple approximate mapping positions between two sets of long sequences, such as between reads and reference genomes, between genomes and between long noisy reads.  
 
|-
 
|-
−
|[http://www.mothur.org/ mothur]
+
|[https://github.com/PacificBiosciences/minorseq/blob/54ac795d7c119d21a4611d91ac458cd3e2e2b30a/doc/INSTALL.md minorseq]
−
|1.8.0, 1.28.0, 1.31.2, 1.32.0, 1.32.1, 1.33.3, 1.38.1
+
|20180314-IGB-gcc-4.9.4
−
|This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.
+
|Minor Variant Calling and Phasing Tools
 
|-
 
|-
−
|[http://veda.cs.uiuc.edu/swan/ MotifScan]
+
|[https://github.com/rajewsky-lab/mirdeep2 mirdeep2]
−
|6
+
|0.0.8-IGB-gcc-4.9.4<br>0.1.3-IGB-gcc-4.9.4
−
|Swan Motif Scanning Software
+
|miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
 
|-
 
|-
−
|[http://faculty.franklin.uga.edu/lliu/content/mp-est?http://faculty.franklin.uga.edu/lliu/content/mp-est? MP-EST]
+
|[http://mitf.cbrc.jp/MitoFates/program.html mitofates]
−
|1.5
+
|1.2-IGB-gcc-4.9.4-Perl-5.24.1
−
|MP-EST estimates species trees from a set of gene trees by maximizing a pseudo-likelihood function. The input data of MP-EST are rooted binary gene trees produced by the maximum likelihood phylogenetic programs RAxML, PHYML, PHYLIP, and PAUP etc. In addition to the gene tree file, a control file must be generated for running MP-EST. The control file contains necessary parameters for running MP-EST.
+
|MitoFates predicts mitochondrial presequence, a cleavable localization signal located in N-terminal, and its cleaved position.
 +
|-
 +
|[https://github.com/tseemann/mlst mlst]
 +
|2.19.0-IGB-gcc-8.2.0-Perl-5.28.1
 +
|Scan contig files against traditional PubMLST typing schemes
 +
|-
 +
|[https://bioinformaticshome.com/tools/rna-seq/descriptions/mmquant.html mmquant]
 +
|1.0.4-IGB-gcc-8.2.0
 +
|A tool to quantiy gene expression. The mmquant algorithm handles multiply mapping reads, i.e., duplicated genes by constructing merged genes.  
 +
|-
 +
|[https://github.com/soedinglab/MMseqs2 MMseqs2]
 +
|10-6d92c
 +
|MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.
 +
|-
 +
|[https://github.com/ddarriba/modeltest modeltest-ng]
 +
|0.1.7
 +
|ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.
 +
|-
 +
|Mono
 +
|
 +
|An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
 
|-
 
|-
−
|[http://www.mpich.org/ mpich]
+
|[https://www.cs.helsinki.fi/group/pssmfind/ MOODS]
−
|3.0.4
+
|1.9.4.1-IGB-gcc-8.2.0-Python-3.7.2
−
|MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
+
|MOODS is a suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds.
 
|-
 
|-
−
|[http://www.mpich.org/ mpich2]
+
|[http://www.mothur.org/ Mothur]
−
|1.4.1p1, 1.5
+
|1.38.1.1<br>1.39.5<br>1.39.5-IGB-gcc-4.9.4<br>1.44.1-IGB-gcc-8.2.0<br>1.47.0-IGB-gcc-8.2.0
−
|MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
+
|Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
 
|-
 
|-
−
|[http://penglab.janelia.org/proj/mRMR/ mrmr]
+
|MPFR
−
|20090420
+
|
−
|mRMR algorithm (minimum Redundancy Maximum Relavance
+
|The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
 
|-
 
|-
−
|[http://msmbuilder.org msmbuilder]
+
|[http://www.mpich.org/ MPICH]
−
|3.5.0
+
|3.0.4-GCC-4.9.4-2.28
−
|MSMBuilder is an application and python library. It builds statistical models for high-dimensional time-series. The particular focus of the package is on the analysis of atomistic simulations of biomolecular dynamics such as protein folding and conformational change.
+
|MPICH v3.x is an open source high-performance MPI 3.0 implementation.It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
 
|-
 
|-
−
|[http://soap.genomics.org.cn/about.html#resource2 msort]
+
|msgpack
−
|1.0
+
|
−
|Msort: a better sort tool; sort text file rows by multiple fields
+
|It's like JSON but smaller and faster.
 +
|-
 +
|[https://github.com/stschiff/msmc msmc]
 +
|1.1.0
 +
|This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences
 
|-
 
|-
−
|[http://alumni.cs.ucr.edu/~yonghui/mstmap.html MSTMap]
+
|[https://www.enterome.com/downloads/ mspminer]
−
|20151202
+
|2.0
−
|MSTMap is a software tool that is capable of constructing genetic linkage maps efficiently and accurately. It can handle various mapping populations including BC1, DH, Hap, and RIL, among others. The tool builds the genetic linkage map by first constructing a Minimum Spanning Tree (MST), and hence the name MSTMap.
+
|MSPminer reconstitutes Metagenomic Species Pan-genomes by binning co-abundant genes across metagenomic samples.
 
|-
 
|-
−
|[http://fletcherpenney.net/multimarkdown/ MultiMarkdown]
+
|[https://github.com/mitoNGS/MToolBox MToolBox]
−
|4.6
+
|1.0-IGB-gcc-4.9.4<br>1.2.1-IGB-gcc-4.9.4
−
|MultiMarkdown, or MMD, is a tool to help turn minimally marked-up plain text into well formatted documents, including HTML, PDF
+
|MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy.
 
|-
 
|-
−
|[https://github.com/ewels/MultiQC multiqc]
+
|[http://multigeneblast.sourceforge.net multigeneblast]
−
|0.7
+
|1.1.12-IGB-gcc-4.9.4
−
|MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
+
|MultiGeneBlast is an open source tool for identification of homologs of multigene modules such as operons and gene clusters. It is based on a reformatting of the FASTA headers of NCBI GenBank protein entries, using which it can track down their source nucleotide and coordinates.
 
|-
 
|-
−
|[http://www.bx.psu.edu/miller_lab/ multiz]
+
|[http://multiqc.info/ MultiQC]
−
|2009-jan-21
+
|0.9-IGB-gcc-4.9.4-Python-2.7.13<br>1.11-IGB-gcc-8.2.0-Python-3.7.2<br>1.14-IGB-gcc-8.2.0-Python-3.7.2<br>1.15-IGB-gcc-8.2.0-Python-3.7.2<br>1.2-IGB-gcc-4.9.4-Python-2.7.13<br>1.6-IGB-gcc-4.9.4-Python-3.6.1<br>1.7-IGB-gcc-4.9.4-Python-3.6.1<br>1.7-IGB-gcc-8.2.0-Python-3.7.2<br>1.9-IGB-gcc-8.2.0-Python-3.7.2
−
|Alignment software
+
|MultiQC searches a given directory for analysis logs and compiles a HTML report. Its a general use tool, perfect for summarising the output from numerous bioinformatics tools.
 
|-
 
|-
 
|[http://mummer.sourceforge.net/ MUMmer]
 
|[http://mummer.sourceforge.net/ MUMmer]
−
|3.23
+
|3.23-IGB-gcc-4.9.4<br>3.23-IGB-gcc-8.2.0<br>4.0.0beta2-IGB-gcc-4.9.4<br>4.0.0beta2-IGB-gcc-8.2.0<br>4.0.0rc1-IGB-gcc-8.2.0
−
|MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. For example, MUMmer 3.0 can find all 20-basepair or longer exact matches between a pair of 5-megabase genomes in 13.7 seconds, using 78 MB of memory, on a 2.4 GHz Linux desktop computer. MUMmer can also align incomplete genomes; it can easily handle the 100s or 1000s of contigs from a shotgun sequencing project, and will align them to another set of contigs or a genome using the NUCmer program included with the system. If the species are too divergent for a DNA sequence alignment to detect similarity, then the PROmer program can generate alignments based upon the six-frame translations of both input sequences.
+
|MUMmer is a system for rapidly aligning entire genomes
 +
|-
 +
|[http://drive5.com/muscle/ MUSCLE]
 +
|3.8.31-IGB-gcc-4.9.4
 +
|MUSCLE is one of the best-performing multiple alignment programs  according to published benchmark tests, with accuracy and speed that are consistently  better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users  learn everything they need to know about MUSCLE in a few minutes—only a handful of  command-line options are needed to perform common alignment tasks. - Homepage: http://drive5.com/muscle/
 +
|-
 +
|[https://www.ks.uiuc.edu/Research/namd/ NAMD]
 +
|20200428
 +
|is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
 +
|-
 +
|[https://github.com/wdecoster/nanopack nanopack]
 +
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
 +
|Easily install all my long read processing and analysis scripts simultaneously.
 +
|-
 +
|[https://github.com/wdecoster/NanoPlot NanoPlot]
 +
|1.18.2-IGB-gcc-4.9.4-Python-3.6.1
 +
|Plotting tool for long read sequencing data and alignments.
 +
|-
 +
|[https://github.com/jts/nanopolish nanopolish]
 +
|0.10.1-IGB-gcc-4.9.4<br>0.10.2-IGB-gcc-4.9.4<br>0.11.0-IGB-gcc-4.9.4<br>0.13.2-IGB-gcc-8.2.0<br>0.6.0-IGB-gcc-4.9.4<br>0.7.1-IGB-gcc-4.9.4<br>0.7.1-IGB-gcc-4.9.4-159d92b<br>0.8.3-IGB-gcc-4.9.4<br>0.8.5-IGB-gcc-4.9.4<br>0.9.0-IGB-gcc-4.9.4
 +
|Software package for signal-level analysis of Oxford Nanopore sequencing data.
 +
|-
 +
|[https://github.com/mroosmalen/nanosv NanoSV]
 +
|1.2.4-IGB-gcc-8.2.0-Python-3.7.2
 +
|NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.
 +
|-
 +
|NASM
 +
|
 +
|NASM: General-purpose x86 assembler
 +
|-
 +
|[https://www.ncbi.nlm.nih.gov/datasets/ ncbi-datasets]
 +
|20220607<br>20221101<br>20240305
 +
|Install and use the NCBI Datasets command line tools
 +
|-
 +
|[https://github.com/kblin/ncbi-genome-download ncbi-genome-download]
 +
|0.2.9-IGB-gcc-4.9.4-Python-3.6.1
 +
|Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago.
 +
|-
 +
|[http://ncbi.github.io/cxx-toolkit/ ncbi-toolkit]
 +
|22-IGB-gcc-8.2.0
 +
|The NCBI Toolkit is a collection of utilities developed for the production and distribution of GenBank, Entrez, BLAST, and related services  by the National Center for Biotechnology Information.
 +
|-
 +
|[https://github.com/ncbi/ncbi-vdb ncbi-vdb]
 +
|2.11.0-IGB-gcc-8.2.0<br>2.8.2-IGB-gcc-4.9.4
 +
|The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
 +
|-
 +
|[http://cran.r-project.org/web/packages/ncdf4 ncdf4]
 +
|1.16-IGB-gcc-4.9.4-R-3.3.3
 +
|This package provides a high-level R interface to data files written using Unidatas netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets.
 +
|-
 +
|[http://nco.sourceforge.net NCO]
 +
|4.7.2-IGB-gcc-4.9.4<br>5.0.1-IGB-gcc-8.2.0
 +
|manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5
 +
|-
 +
|ncurses
 +
|
 +
|The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
 +
|-
 +
|[http://meteora.ucsd.edu/~pierce/ncview_home_page.html ncview]
 +
|2.1.7-IGB-gcc-8.2.0
 +
|Ncview is a visual browser for netCDF format files.Typically you would use ncview to get a quick and easy, push-buttonlook at your netCDF files. You can view simple movies of the data,view along various dimensions, take a look at the actual data values,change color maps, invert the data, etc.
 +
|-
 +
|[http://www.unidata.ucar.edu/software/netcdf/ netCDF]
 +
|4.4.1.1-IGB-gcc-4.9.4<br>4.7.2-IGB-gcc-8.2.0
 +
|NetCDF (network Common Data Form) is a set of software libraries  and machine-independent data formats that support the creation, access, and sharing of array-oriented  scientific data.
 +
|-
 +
|[http://www.unidata.ucar.edu/software/netcdf/ netCDF-Fortran]
 +
|4.4.1-IGB-gcc-4.9.4<br>4.5.2-IGB-gcc-8.2.0
 +
|NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
 +
|-
 +
|[https://ccl.northwestern.edu/netlogo/ NetLogo]
 +
|5.2.1<br>6.0.3
 +
|NetLogo is a multi-agent programmable modeling environment. It is used by many tens of thousands of students, teachers and researchers worldwide.
 
|-
 
|-
−
|[http://www.drive5.com/muscle/ muscle]
+
|[http://www.lysator.liu.se/~nisse/nettle/ nettle]
−
|3.8.31
+
|3.3-IGB-gcc-4.9.4
−
|MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds.
+
|Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.
 
|-
 
|-
−
|[http://www.broadinstitute.org/cancer/cga/mutect muTect]
+
|[https://www.nextflow.io/ nextflow]
−
|1.1.4
+
|0.25.7-Java-1.8.0_121<br>0.26.3-Java-1.8.0_152<br>18.10.1-Java-1.8.0_152<br>19.07.0-Java-1.8.0_152<br>20.01.0-Java-1.8.0_152<br>21.03.0-Java-1.8.0_152<br>21.03.0-Java-1.8.0_201<br>21.04.1-Java-1.8.0_152<br>21.06.0-edge-Java-1.8.0_152<br>22.09.7-Java-11.0.5<br>22.10.1-Java-15.0.1<br>22.10.6-Java-15.0.1<br>23.10.0-Java-15.0.1
−
|MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
+
|Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.  
 
|-
 
|-
−
|[https://www.broadinstitute.org/cancer/cga/mutsig MutSigCV]
+
|[https://github.com/Nextomics/NextPolish NextPolish]
−
|1.4
+
|1.4.0-IGB-gcc-8.2.0
−
|MutSig stands for 'Mutation Significance'.  MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
+
|NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both.
 
|-
 
|-
−
|[http://enve-omics.ce.gatech.edu/mytaxa/ mytaxa]
+
|[https://github.com/nf-core/tools nf-core]
−
|0.1.0
+
|1.6-IGB-gcc-4.9.4-Python-3.6.1<br>2.7.2-IGB-gcc-8.2.0-Python-3.10.1
−
|MyTaxa represents a new algorithm that extends the Average Amino Acid Identity (AAI) concept (Konstantinidis and Tiedje, PNAS 2005) to identify the taxonomic affiliation of a query genome sequence or a sequence of a contig assembled from a metagenome, including short sequences (e.g., 100-1,000nt long), and to classify sequences representing novel taxa at three levels (whenever possible), i.e., species, genus and phylum.
+
|A community effort to collect a curated set of analysis pipelines built using Nextflow.
 
|-
 
|-
−
|[http://www.ks.uiuc.edu/Research/namd/ NAMD]
+
|NGS
−
|2.10b2
+
|
−
|AMD, recipient of a 2002 Gordon Bell Award and a 2012 Sidney Fernbach Award, is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of cores for typical simulations and beyond 200,000 cores for the largest simulations. NAMD uses the popular molecular graphics program VMD for simulation setup and trajectory analysis, but is also file-compatible with AMBER, CHARMM, and X-PLOR. NAMD is distributed free of charge with source code. You can build NAMD yourself or download binaries for a wide variety of platforms. Our tutorials show you how to use NAMD and VMD for biomolecular modeling.
+
|NGS is a new, domain-specific API for accessing reads, alignments and pileupsproduced from Next Generation Sequencing.
 
|-
 
|-
−
|[https://github.com/jgurtowski/nanocorr nanocorr]
+
|[https://github.com/parklab/NGSCheckMate NGSCheckMate]
−
|20160407
+
|20190507-IGB-gcc-8.2.0-Python-2.7.18
−
|Error correction for oxford nanopore reads
+
|NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual. It analyzes various types of NGS data files including (but not limited to) whole genome sequencing (WGS), whole exome sequencing (WES), RNA-seq, ChIP-seq, and targeted sequencing of various depths.
 
|-
 
|-
−
|[https://github.com/jts/nanocorrect/ nanocorrect]
+
|[https://github.com/fgvieira/ngsF ngsF]
−
|20150421
+
|1.2.0-IGB-gcc-8.2.0
−
|A prototype nanopore correction pipeline.
+
|ngsF is a program to estimate per-individual inbreeding coefficients under a probabilistic framework that takes the uncertainty of genotype's assignation into account. It avoids calling genotypes by using genotype likelihoods or posterior probabilities.
 
|-
 
|-
−
|[https://github.com/jts/nanopolish nanopolish]
+
|[https://github.com/fgvieira/ngsF-HMM ngsF-HMM]
−
|0.5.0, 0.6-dev, 0.6.0
+
|20200722-IGB-gcc-8.2.0
−
|A nanopore consensus algorithm using a signal-level hidden Markov model.
+
|ngsF-HMM is a program to estimate per-individual inbreeding tracts using a two-state Hidden Markov Model (HMM).  
 +
|-
 +
|[https://github.com/fgvieira/ngsLD ngsLD]
 +
|1.2.0-IGB-gcc-8.2.0
 +
|ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account. It does so by avoiding genotype calling and using genotype likelihoods or posterior probabilities.
 
|-
 
|-
−
|[http://nco.sourceforge.net/ nco]
+
|[https://ninja-build.org/ ninja]
−
|4.4.2, 4.4.8
+
|1.8.2-IGB-gcc-4.9.4
−
|NCO manipulates data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. It also exploits the geophysical expressivity of many CF (Climate & Forecast) metadata conventions, the flexible description of physical dimensions translated by UDUnits, the network transparency of OPeNDAP, the storage features (e.g., compression, chunking, groups) of HDF (the Hierarchical Data Format), and many powerful mathematical and statistical algorithms of GSL (the GNU Scientific Library). NCO is fast, powerful, and free.
+
|Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible.
 
|-
 
|-
−
|[http://www.unidata.ucar.edu/software/netcdf/ netcdf]
+
|[https://github.com/TravisWheelerLab/NINJA NINJA]
−
|4.3.1.1, 4.3.3.1
+
|0.97-IGB-gcc-4.9.4
−
|NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
+
|Nearly Infinite Neighbor Joining Application
 
|-
 
|-
−
|[https://ccl.northwestern.edu/netlogo/ netlogo]
+
|[https://ninja-build.org/ Ninja]
−
|5.3.1
+
|1.9.0-IGB-gcc-4.9.4
−
|NetLogo is a multi-agent programmable modeling environment.
+
|Ninja is a small build system with a focus on speed.
 
|-
 
|-
−
|[http://networkx.github.io/documentation/latest/install.html networkx]
+
|[https://github.com/nltk/nltk nltk]
−
|1.9.1
+
|3.5-IGB-gcc-4.9.4-Python-3.6.1<br>3.5-IGB-gcc-8.2.0-Python-3.7.2
−
|networkX is a Python language software package for the creation, manipulation, and study of the structure, dynamics, and function of complex networks.
+
|NLTK -- the Natural Language Toolkit -- is a suite of open source Python modules, data sets, and tutorials supporting research and development in Natural Language Processing.
 
|-
 
|-
−
|[http://www.nextflow.io/ nextflow]
+
|[http://nodejs.org nodejs]
−
|0.15.6, 0.16.4, 0.17.3, 0.22.5, 0.22.6
+
|10.16.2-IGB-gcc-4.9.4<br>14.15.0-IGB-gcc-8.2.0<br>9.9.0-IGB-gcc-4.9.4
−
|Nextflow is a fluent DSL modelled around the UNIX pipe concept, that simplifies writing parallel and scalable pipelines in a portable manner.
+
|Node.js is a platform built on Chromes JavaScript runtime  for easily building fast, scalable network applications. Node.js uses an  event-driven, non-blocking I/O model that makes it lightweight and efficient,  perfect for data-intensive real-time applications that run across distributed devices.
 
|-
 
|-
−
|[https://github.com/shenlab-sinai/ngsplot ngsplot]
+
|[https://github.com/lmrodriguezr/nonpareil nonpareil]
−
|2.61
+
|3.3.4-IGB-gcc-8.2.0
−
|ngs.plot is a program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.
+
|Estimate average coverage and create Nonpareil curves for metagenomic datasets.
 
|-
 
|-
−
|[http://nodejs.org/ node]
+
|[http://github.com/wolever/nose-parameterized nose-parameterized]
−
|0.10.28
+
|0.6.0-IGB-gcc-4.9.4-Python-2.7.13
−
|Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications.
+
|Parameterized testing with any Python test framework.
 
|-
 
|-
−
|[http://www.novocraft.com novocraft]
+
|[http://www.novocraft.com/ novocraft]
−
|2.08, 2.08.02, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 3.02
+
|3.08.00
 
|Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms.
 
|Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms.
 
|-
 
|-
−
|[https://github.com/numba/numba numba]
+
|[https://github.com/npm/cli npm]
−
|0.32.0
+
|v7.20.0-IGB-gcc-4.9.4
 +
|the package manager for JavaScript
 +
|-
 +
|[http://nucleoatac.readthedocs.io/en/latest/ NucleoATAC]
 +
|0.3.4-IGB-gcc-4.9.4-Python-2.7.13
 +
|NucleoATAC is a python package for calling nucleosome positions and occupancy using ATAC-Seq data. Functions for calling nucleosomes are included in the nucleoatac command-line function. NucleoATAC also includes other utlities for working with ATAC-seq data under the pyatac function.
 +
|-
 +
|numactl
 +
|
 +
|The numactl program allows you to run your application program on specific cpus and memory nodes.It does this by supplying a NUMA memory policy to the operating system before running your program.The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
 +
|-
 +
|[http://numba.pydata.org/ numba]
 +
|0.34.0-IGB-gcc-4.9.4-Python-2.7.13<br>0.34.0-IGB-gcc-4.9.4-Python-3.6.1<br>0.35.0-IGB-gcc-4.9.4-Python-2.7.13<br>0.52.0-IGB-gcc-8.2.0-Python-3.7.2<br>0.55.2-IGB-gcc-8.2.0-Python-3.7.2<br>0.59.0-IGB-gcc-8.2.0-Python-3.10.1
 
|Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.
 
|Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.
 
|-
 
|-
−
|[http://www.ebi.ac.uk/~zerbino/oases/ oases-kmer245]
+
|numpy
−
|0.2.8
+
|
−
|Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
+
|The fundamental package for scientific computing with Python
 
|-
 
|-
−
|[http://www.ebi.ac.uk/~zerbino/oases/ oases]
+
|[http://www.nwchem-sw.org NWChem]
−
|0.2.8
+
|6.6.revision27746-IGB-gcc-4.9.4-Python-2.7.13
−
|Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
+
|NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.
 
|-
 
|-
−
|[http://metabarcoding.org/obitools/doc/welcome.html OBITools]
+
|[https://git.metabarcoding.org/obitools/obitools3 OBITools3]
−
|1.2.9
+
|3.0.0b42-IGB-gcc-8.2.0-Python-3.7.2
−
|The OBITools package is a set of programs specifically designed for analyzing NGS data in a DNA metabarcoding context, taking into account taxonomic information.
+
|The OBITools3: A package for the management of analyses and data in DNA metabarcoding  
 
|-
 
|-
−
|[http://ocaml.org ocaml]
+
|[http://ocaml.org/ OCaml]
−
|4.01
+
|4.05.0-IGB-gcc-4.9.4
−
|Ocaml Compiler
+
|OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.
 
|-
 
|-
−
|[http://www.regulatory-genomics.org/odin-2 ODIN]
+
|[https://github.com/luntergroup/octopus octopus]
−
|0.4.1
+
|0.6.3-beta-IGB-gcc-8.2.0
−
|ODIN is an HMM-based approach to detect and analyse differential peaks in pairs of ChIP-seq data. ODIN performs genomic signal processing, peak calling and p-value calculation in an integrated framework. ODIN is tailored for the comparison of two ChIP-seq signals without replicates.
+
|Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner.  
 
|-
 
|-
−
|OLB
+
|[https://github.com/brianbeliveau/OligoMiner OligoMiner]
−
|1.9.4
+
|20181123-IGB-gcc-4.9.4
−
|adds environmental variables to qiime and qiime
+
|A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
 
|-
 
|-
−
|[http://oligotyping.org/ oligotyping]
+
|[https://github.com/dovetail-genomics/Omni-C Omni-C]
−
|1.4
+
|20210526-IGB-gcc-8.2.0-Python-3.7.2
−
|a novel computational method that can help microbial ecologists to investigate concealed diversity at an extremely precise level within their closely related organisms by utilizing very subtle variations among 16S Ribosomal RNA gene pyro-tag sequences.
+
|The Dovetail™ Omni-C™ library uses a sequence-independent endonuclease for chromatin digestion prior to proximity ligation and library generation.
 
|-
 
|-
−
|[http://opam.ocaml.org opam]
+
|[https://github.com/nanoporetech/ont_fast5_api ont-fast5-api]
−
|1.1.1
+
|3.1.5-IGB-gcc-8.2.0-Python-3.7.2<br>3.3.0-IGB-gcc-8.2.0-Python-3.7.2
−
|Package manager for OCaml
+
|ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format.
 
|-
 
|-
−
|[http://openbabel.org openbabel]
+
|[http://openbabel.org OpenBabel]
−
|2.3.1
+
|3.0.0-IGB-gcc-8.2.0
 
|Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
 
|Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
 
|-
 
|-
−
|[http://www.openblas.net/ OpenBLAS]
+
|OpenBLAS
−
|0.2.14, 0.2.15, 0.2.19
+
|
−
|OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13
+
|OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
 +
|-
 +
|[http://opencv.org/ OpenCV]
 +
|3.1.0-IGB-gcc-4.9.4-Python-2.7.13<br>3.3.0-IGB-gcc-4.9.4-Python-3.6.1<br>4.5.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.
 +
|-
 +
|[http://www.open-mpi.org/ OpenMPI]
 +
|2.1.0-GCC-4.9.4-2.28<br>4.0.0-GCC-8.2.0-2.32
 +
|The Open MPI Project is an open source MPI-3 implementation.
 +
|-
 +
|OpenPGM
 +
|
 +
|OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.
 
|-
 
|-
−
|[http://www.open-mpi.org/ openmpi-intel]
+
|[https://opensfm.org/ OpenSfM]
−
|1.6.3
+
|0.5.1-IGB-gcc-8.2.0-Python-3.7.2
−
|The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
+
|OpenSfM is a Structure from Motion library written in Python. The library serves as a processing pipeline for reconstructing camera poses and 3D scenes from multiple images.
 
|-
 
|-
−
|[http://www.open-mpi.org/ openmpi]
+
|[http://www.openssl.org/ OpenSSL]
−
|1.4.3, 1.6.3, 1.8.8
+
|1.1.1m-IGB-gcc-8.2.0
−
|The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
+
|The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1)  protocols as well as a full-strength general purpose cryptography library.  
 
|-
 
|-
−
|[http://www.orthomcl.org/orthomcl/ orthomcl]
+
|[https://github.com/davidemms/OrthoFinder OrthoFinder]
−
|2.0.2, 2.0.7
+
|2.2.7<br>2.3.7-IGB-gcc-4.9.4<br>2.5.4-IGB-gcc-8.2.0
−
|OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. It provides not only groups shared by two or more species/genomes, but also groups representing species-specific gene expansion families. So it serves as an important utility for automated eukaryotic genome annotation. OrthoMCL starts with reciprocal best hits within each genome as potential in-paralog/recent paralog pairs and reciprocal best hits across any two genomes as potential ortholog pairs. Related proteins are interlinked in a similarity graph. Then MCL (Markov Clustering algorithm,Van Dongen 2000; www.micans.org/mcl) is invoked to split mega-clusters. This process is analogous to the manual review in COG construction. MCL clustering is based on weights between each pair of proteins, so to correct for differences in evolutionary distance the weights are normalized before running MCL.
+
|OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthologs and orthogroups, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees.  
 
|-
 
|-
−
|[http://wasabiapp.org/software/pagan/ pagan]
+
|[http://orthomcl.org/ OrthoMCL]
−
|20150723
+
|2.0.9-IGB-gcc-4.9.4-Perl-5.24.1
 +
|OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. - Homepage: http://orthomcl.org/
 +
|-
 +
|[https://github.com/jacirrone/OutPredict OutPredict]
 +
|1.0.0-IGB-gcc-8.2.0-Python-3.7.2
 +
|This repository contains OutPredict, a python developed Method for Predicting Out-of-sample Data in Time Series and Steady State data as well as to predict Causal connections from transcription factors to genes.
 +
|-
 +
|[https://github.com/jinfeihan57/p7zip/ p7zip]
 +
|17.04-IGB-gcc-8.2.0
 +
|p7zip is a quick port of 7z.exe and 7za.exe (CLI version of7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.
 +
|-
 +
|[https://github.com/swarris/Pacasus Pacasus]
 +
|1.2-IGB-gcc-4.9.4-Python-2.7.13
 +
|Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification.
 +
|-
 +
|[http://wasabiapp.org/software/pagan PAGAN]
 +
|20150723-IGB-gcc-4.9.4
 
|PAGAN is a general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. However, graphs also allow describing the uncertainty in input sequences and modelling e.g. homopolymer errors in Roche 454 reads, or representing inferred ancestral sequences against which other sequences can then be aligned. PAGAN is still under development and will hopefully evolve to an easy-to-use, general-purpose method for phylogenetic sequence alignment.
 
|PAGAN is a general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. However, graphs also allow describing the uncertainty in input sequences and modelling e.g. homopolymer errors in Roche 454 reads, or representing inferred ancestral sequences against which other sequences can then be aligned. PAGAN is still under development and will hopefully evolve to an easy-to-use, general-purpose method for phylogenetic sequence alignment.
 
|-
 
|-
−
|[https://www.sanger.ac.uk/resources/software/pagit/ pagit]
+
|[https://www.sanger.ac.uk/tool/pagit/ pagit]
−
|1.64
+
|1.0
 
|Tools to generate automatically high quality sequence by ordering contigs, closing gaps, correcting sequence errors and transferring annotation.
 
|Tools to generate automatically high quality sequence by ordering contigs, closing gaps, correcting sequence errors and transferring annotation.
 +
|-
 +
|[https://github.com/4dn-dcic/pairix pairix]
 +
|0.3.7-IGB-gcc-8.2.0
 +
|Pairix is a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates.
 +
|-
 +
|[https://github.com/mirnylab/pairtools pairtools]
 +
|0.3.0-IGB-gcc-4.9.4-Python-3.6.1<br>1.0.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment.
 
|-
 
|-
 
|[http://www.bork.embl.de/pal2nal/ pal2nal]
 
|[http://www.bork.embl.de/pal2nal/ pal2nal]
−
|14
+
|14-IGB-gcc-4.9.4
−
|PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment. The program automatically assigns the corresponding codon sequence even if the input DNA sequence has mismatches with the input protein sequence, or contains UTRs, polyA tails.
+
|PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment.
 +
|-
 +
|[http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
 +
|4.9e-IGB-gcc-4.9.4
 +
|PAML is a package of programs for phylogenetic  analyses of DNA or protein sequences using maximum likelihood. - Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
 +
|-
 +
|[https://github.com/neufeld/pandaseq PANDAseq]
 +
|2.11-IGB-gcc-4.9.4
 +
|PANDAseq assembles Illumina Solexa overlapping pair-end reads. - Homepage: https://github.com/neufeld/pandaseq
 
|-
 
|-
−
|[http://abacus.gene.ucl.ac.uk/software/paml.html paml]
+
|[http://pandoc.org pandoc]
−
|4.4, 4.8
+
|2.2.3.2
−
|PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. It is maintained and distributed for academic use free of charge by Ziheng Yang.
+
|If you need to convert files from one markup format into another, pandoc is your swiss-army knife
 
|-
 
|-
−
|[https://github.com/neufeld/pandaseq pandaseq]
+
|Pango
−
|2.8, 2.10
+
|
−
|a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
+
|Pango is a library for laying out and rendering of text, with an emphasis on internationalization.Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in thecontext of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
 
|-
 
|-
−
|[http://www.pantherdb.org/downloads/index.jsp panther]
+
|[https://github.com/cov-lineages/pangolin pangolin]
−
|1.03
+
|2.3.2-IGB-gcc-8.2.0-Python-3.7.2<br>2.4.2-IGB-gcc-8.2.0-Python-3.7.2
−
|score protein sequences against the entire PANTHER HMM library and analyze your sequences
+
|Phylogenetic Assignment of Named Global Outbreak LINeages
 
|-
 
|-
−
|[http://cucis.ece.northwestern.edu/projects/PnetCDF/ parallel-netcdf]
+
|[https://developer.nvidia.com/clara-parabricks parabricks]
−
|1.4.1
+
|3.1.0-IGB-gcc-8.2.0-Python-3.7.2<br>3.7.0
−
|Parallel netCDF (PnetCDF) is an I/O library that supports data access to netCDF files in parallel, a collaborative work of Northwestern University and Argonne National Laboratory.
+
|NVIDIA Clara™ Parabricks is a computational framework supporting genomics applications from DNA to RNA. It employs NVIDIA’s CUDA, HPC, AI, and data analytics stacks to build GPU accelerated libraries, pipelines, and reference application workflows for primary, secondary, and tertiary analysis.
 
|-
 
|-
 
|[https://www.gnu.org/software/parallel/ parallel]
 
|[https://www.gnu.org/software/parallel/ parallel]
−
|20150322
+
|20170622-IGB-gcc-4.9.4<br>20200822-IGB-gcc-8.2.0
−
|GNU parallel is a shell tool for executing jobs in parallel using one or more computers. A job can be a single command or a small script that has to be run for each of the lines in the input.
+
|parallel: GNU parallel is a shell tool for executing jobs in parallel using one or more computers.  
 +
|-
 +
|[https://github.com/PacificBiosciences/pb-assembly pb-assembly]
 +
|0.0.6<br>0.0.8
 +
|PacBio Assembly Tool Suite
 +
|-
 +
|[https://github.com/PacificBiosciences/pbAA pbaa]
 +
|1.0.3.0
 +
|PacBio Amplicon Analysis (pbaa) separates complex mixtures of amplicon targets from genomic samples. The pbaa application is designed to cluster and generate high-quality consensus sequences from HiFi reads.
 +
|-
 +
|[https://github.com/PacificBiosciences/pbbam pbbam]
 +
|1.0.7-IGB-gcc-8.2.0
 +
|The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.
 
|-
 
|-
−
|[http://bioinformatics.ai.sri.com/ptools/ pathway-tools]
+
|[https://github.com/PacificBiosciences/ccs pbccs]
−
|16.5
+
|4.0<br>6.4.0
−
|Pathway Tools is a comprehensive systems-biology software system that is associated with the BioCyc database collection and supports several use cases in bioinformatics.
+
|ccs takes multiple subreads of the same SMRTbell molecule and combines them using a statistical model to produce one highly accurate consensus sequence, also called HiFi read, with base quality values.
 
|-
 
|-
−
|[http://sourceforge.net/p/pb-jelly/wiki/Home/ PBJelly]
+
|[https://github.com/PacificBiosciences/pbbioconda/wiki/Improved-Phased-Assembler pbipa]
−
|12.9.14
+
|1.3.0<br>1.3.2
−
|PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. Each step in PBJelly’s workflow can be run on a cluster, thus parallelizing the gap filling process for rapid turn around, even for very large eukaryotic genomes.
+
|Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies.
 +
|-
 +
|[https://github.com/PacificBiosciences/pbmm2 pbmm2]
 +
|1.12.0<br>1.4.0
 +
|pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments.  
 
|-
 
|-
 
|[http://compression.ca/pbzip2/ pbzip2]
 
|[http://compression.ca/pbzip2/ pbzip2]
−
|1.1.12
+
|1.1.13-IGB-gcc-4.9.4<br>1.1.13-IGB-gcc-8.2.0
−
|PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines. The output of this version is fully compatible with bzip2 v1.0.2 or newer (ie: anything compressed with pbzip2 can be decompressed with bzip2). PBZIP2 should work on any system that has a pthreads compatible C++ compiler (such as gcc). It has been tested on: Linux, Windows (cygwin & MinGW), Solaris, Tru64/OSF1, HP-UX, OS/2, OSX, and Irix.
+
|PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines.
 +
|-
 +
|[https://github.com/Rosemeis/pcangsd/ pcangsd]
 +
|0.9-IGB-gcc-4.9.4-Python-2.7.13<br>20220330-IGB-gcc-8.2.0-Python-3.7.2
 +
|Framework for analyzing low-depth next-generation sequencing (NGS) data in heterogeneous/structured populations using principal component analysis (PCA).  
 +
|-
 +
|PCRE
 +
|
 +
|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
 +
|-
 +
|PCRE2
 +
|
 +
|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
 +
|-
 +
|[https://github.com/tbischler/PEAKachu PEAKachu]
 +
|0.1.0-IGB-gcc-8.2.0-Python-3.7.2
 +
|Peak calling tool for CLIP-seq data
 +
|-
 +
|[http://sco.h-its.org/exelixis/web/software/pear/ PEAR]
 +
|0.9.8-IGB-gcc-4.9.4
 +
|PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. - Homepage: http://sco.h-its.org/exelixis/web/software/pear/
 +
|-
 +
|[https://github.com/soedinglab/PEnG-motif PEnG-motif]
 +
|1.0.1
 +
|PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.
 +
|-
 +
|[https://github.com/shawnzhangyx/PePr PePr]
 +
|1.1.21-IGB-gcc-4.9.4-Python-2.7.13
 +
|PePr is a ChIP-Seq Peak-calling and Prioritization pipeline that uses a sliding window approach and models read counts across replicates and between groups with a negative binomial distribution.
 +
|-
 +
|[https://github.com/cschin/Peregrine Peregrine]
 +
|1.5.4
 +
|Peregrine & SHIMMER Genome Assembly Toolkit
 
|-
 
|-
−
|[https://github.com/wtsi-npg/pb_calibration pb_calibration]
+
|[http://perfsuite.ncsa.illinois.edu/ perfsuite]
−
|10.21, 10.22
+
|1.1.4-IGB-gcc-4.9.4
−
|Filter and calibration programs for Illumina sequencing data (in BAM files).
+
|PerfSuite is a collection of tools, utilities, and libraries for software performance analysis where the primary design goals are ease of use, comprehensibility, interoperability, and simplicity. This software can provide a good "entry point" for more detailed performance analysis and can help point the way towards selecting other tools and/or techniques using more specialized software if necessary (for example, tools/libraries from academic research groups or third-party commercial software).  
 
|-
 
|-
−
|[http://www.pcre.org/ pcre]
+
|[http://www.perl.org/ Perl]
−
|8.37
+
|5.24.1-IGB-gcc-4.9.4<br>5.24.1-IGB-gcc-4.9.4-bare<br>5.26.1-IGB-gcc-4.9.4-unthreaded<br>5.28.1-IGB-gcc-8.2.0
−
|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE has its own native API, as well as a set of wrapper functions that correspond to the POSIX regular expression API. The PCRE library is free, even for building proprietary software.
+
|Larry Wall's Practical Extraction and Report Language
 
|-
 
|-
−
|[http://www.ebi.ac.uk/research/bertone/software peaksplitter]
+
|[ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/README pfamscan]
−
|1.0
+
|1.6-IGB-gcc-4.9.4-Perl-5.24.1
−
|Subdivision of ChIP-seq/ChIP-chip regions into discrete signal peaks
+
|This readme should help you get started with "pfam_scan.pl", which is for usewith the HMMER3 version of HMMER.
 +
|-
 +
|[http://bioinfadmin.cs.ucl.ac.uk/downloads/pfilt/ pfilt]
 +
|1.5-IGB-gcc-8.2.0
 +
|The pfilt program is designed to mask out (i.e. replace amino acid characterswith Xs) regions of low complexity, coiled-coil regions and more regions withextremely biased amino acid compositions.
 +
|-
 +
|[https://github.com/sib-swiss/pftools3 pftoolsV3]
 +
|3.2.12-IGB-gcc-8.2.0
 +
|A suite of tools to build and search generalized profiles (protein and DNA).
 +
|-
 +
|[http://www.cmpg.unibe.ch/software/PGDSpider/ PGDSpider]
 +
|2.1.1.5-Java-1.8.0_201
 +
|PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances).
 +
|-
 +
|[https://github.com/pgmpy/pgmpy pgmpy]
 +
|20180320-IGB-gcc-4.9.4-Python-3.6.1
 +
|pgmpy is a python library for working with Probabilistic Graphical Models.
 
|-
 
|-
−
|[http://www.exelixis-lab.org/web/software/pear pear]
+
|[https://github.com/kundajelab/phantompeakqualtools Phantompeaktools]
−
|0.9.5
+
|1.2-IGB-gcc-4.9.4-R-3.4.1
−
|an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
+
|Custom SPP for Phantompeaktools
 
|-
 
|-
−
|[http://penncnv.openbioinformatics.org/en/latest/ PennCNV]
+
|Phantompeaktools-spp
−
|1.0.3
+
|
−
|PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.
+
|Custom SPP for Phantompeaktools
 
|-
 
|-
−
|[http://penncnv.openbioinformatics.org/en/latest/ penncnv]
+
|[https://sourceforge.net/projects/phispy PhiSpy]
−
|1.0.3
+
|2.3-IGB-gcc-4.9.4-Python-2.7.13
−
|PennCNV is a free software tool for Copy Number Variation (CNV) detection from SNP genotyping arrays. Currently it can handle signal intensity data from Illumina and Affymetrix arrays. With appropriate preparation of file format, it can also handle other types of SNP arrays and oligonucleotide arrays.
+
|A novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies
 
|-
 
|-
−
|perfsuite
+
|[https://phobius.sbc.su.se/data.html phobius]
−
|1.0.0(20)
+
|1.01
−
|ERROR:102: Tcl command execution failed: set _description "PerfSuite is a collection of tools, utilities, and libraries for software performance analysis where the primary design goals are ease of use, comprehensibility, interoperability, and simplicity. This software can provide a good "entry point" for more detailed performance analysis and can help point the way towards selecting other tools and/or techniques using more specialized software if necessary (for example, tools/libraries from academic research groups or third-party commercial software)."
+
|A combined transmembrane topology and signal peptide predictor
 
|-
 
|-
−
|[http://www.perl.org perl]
+
|[http://www.phrap.org/consed/consed.html#howToGet phrap]
−
|5.14.2, 5.16.1, 5.20.1
+
|1.090518-IGB-gcc-8.2.0
−
|Perl 5 is a highly capable, feature-rich programming language with over 25 years of development. Perl 5 runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
+
|A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)
 
|-
 
|-
−
|[ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/ pfamscan]
+
|[https://github.com/HRGV/phyloFlash phyloFlash]
−
|1.0
+
|3.3-IGB-gcc-4.9.4
−
|PFamscan
+
|phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset.
 
|-
 
|-
−
|[ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/ PfamScan]
+
|[https://github.com/biobakery/phylophlan phylophlan]
−
|1.5
+
|3.0.1-IGB-gcc-8.2.0-Python-3.7.2<br>3.0.3-IGB-gcc-8.2.0-Python-3.7.2
−
|search a FASTA file against a library of Pfam HMMs
+
|PhyloPhlAn 3.0 is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
 
|-
 
|-
−
|[https://code.google.com/p/phantompeakqualtools/ phantompeakqualtools]
+
|[https://bitbucket.org/nsegata/phylophlan/wiki/phylophlan2 phylophlan2]
−
|1.1
+
|0.34-IGB-gcc-4.9.4-Python-3.6.1
−
|This package computes quick but highly informative enrichment and quality measures for ChIP-seq/DNase-seq/FAIRE-seq/MNase-seq data. It can also be used to obtain robust estimates of the predominant fragment length or characteristic tag shift values in these assays.
+
|PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
 
|-
 
|-
−
|[http://compgen.bscb.cornell.edu/phast/ phast]
+
|[https://github.com/gjospin/PhyloSift PhyloSift]
−
|1.3
+
|1.0.0_01-IGB-gcc-4.9.4-Perl-5.24.1
−
|PHAST is a freely available software package for comparative and evolutionary genomics. It consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations (see left panel). For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences.
+
|PhyloSift is a suite of software tools to conduct phylogeneticanalysis of genomes and metagenomes.
 
|-
 
|-
−
|[https://sourceforge.net/projects/phispy/ phispy]
+
|[http://broadinstitute.github.io/picard/ picard]
−
|2.3
+
|1.77-Java-1.8.0_152<br>2.10.1-Java-1.8.0_152<br>2.27.5-Java-1.8.0_201<br>2.9.0-Java-1.8.0_121<br>2.9.4-Java-1.8.0_121
−
|PhiSpy: A novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies
+
|A set of tools (in Java) for working with next generation sequencing data in the BAM  (http://samtools.github.io/hts-specs) format.
 
|-
 
|-
−
|[http://www.phrap.com/phred/ phred]
+
|[http://picrust.github.io/picrust/ PICRUSt]
−
|0.020425.c
+
|1.1.1-IGB-gcc-4.9.4-Python-2.7.13<br>1.1.3-IGB-gcc-4.9.4-Python-2.7.13
−
|Phred is a base-calling program for DNA sequence traces. Phred reads DNA sequence chromatogram files and analyzes the peaks to call bases, assigning quality scores (Phred scores) to each base call.
+
|PICRUSt (pronounced pie crust) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.
 
|-
 
|-
−
|[https://github.com/martinwu/Phyla_AMPHORA phyla_amphora]
+
|[https://github.com/picrust/picrust2 PICRUSt2]
−
|1.0
+
|2.3.0-b-IGB-gcc-8.2.0-Python-3.7.2<br>2.4.1-IGB-gcc-8.2.0-Python-3.7.2
−
|A Phylum-specific Automated Phylogenomic Inference Pipeline for Bacterial Sequences.
+
|PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.
 
|-
 
|-
−
|[http://evolution.genetics.washington.edu/phylip.html phylip]
+
|[http://zlib.net/pigz/ pigz]
−
|3.69
+
|2.3.4-IGB-gcc-4.9.4<br>2.4-IGB-gcc-8.2.0
−
|PHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees). Methods that are available in the package include parsimony, distance matrix, and likelihood methods, including bootstrapping and consensus trees. Data types that can be handled include molecular sequences, gene frequencies, restriction sites and fragments, distance matrices, and discrete characters.
+
|pigz, which stands for parallel implementation of gzip, is a fully  functional replacement for gzip that exploits multiple processors and multiple cores  to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib  and pthread libraries.  
 
|-
 
|-
−
|[http://compbio.mit.edu/PhyloCSF phylocsf]
+
|[http://pillow.readthedocs.org/ Pillow]
−
|may-16-2014
+
|5.1.0-IGB-gcc-4.9.4-Python-2.7.13<br>5.1.0-IGB-gcc-4.9.4-Python-3.6.1
−
|Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding region
+
|Pillow is the friendly PIL fork by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
 
|-
 
|-
−
|[https://bitbucket.org/nsegata/phylophlan/wiki/Home phylophlan]
+
|[https://github.com/broadinstitute/pilon pilon]
−
|1.1.0
+
|1.22-Java-1.8.0_121<br>1.23-Java-1.8.0_152
−
|PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. The pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations.
+
|Pilon is a software tool which can be used to:- Automatically improve draft assemblies- Find variation among strains, including large event detection
 
|-
 
|-
−
|phylosift
+
|[http://smithlabresearch.org/software/piranha/ piranha]
−
|1.0.1
+
|1.2.1-IGB-gcc-4.9.4
−
|PhyloSift is a suite of software tools to conduct phylogenetic analysis of genomes and metagenomes. Using a reference database of protein sequences, PhyloSift can scan new sequences against that database for homologs and identify the phylogenetic relationship of the new sequence to the database sequences. During this procedure, high quality alignments of codon and
+
|iranha is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.  
 
|-
 
|-
−
|phymmbl
+
|[https://genie.weizmann.ac.il/pubs/mir07/mir07_exe.html PITA]
−
|4.0(20)
+
|6-IGB-gcc-4.9.4
−
|ERROR:102: Tcl command execution failed: set _description "Phymm, a new classification approach for metagenomics data which uses interpolated Markov models (IMMs) to taxonomically classify DNA sequences, can accurately classify reads as short as 100 bp. Its accuracy for short reads represents a significant leap forward over previous composition-based classification methods. PhymmBL (rhymes with "thimble"), the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy."
+
|The PITA executable allows you to identify and score microRNA targets on UTRs.
 
|-
 
|-
−
|[http://broadinstitute.github.io/picard/ picard-tools]
+
|pixman
−
|1.34, 1.73, 1.90, 1.131, 1.141, 2.1.0, 2.4.1
+
|
−
|A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
+
|Pixman is a low-level software library for pixel manipulation, providing features such as imagecompositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
 
|-
 
|-
−
|[http://picrust.github.io/picrust/ picrust]
+
|pkg-config
−
|1.0.0, devel
+
|
−
|PICRUSt (pronounced 'pie crust') is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.
+
|pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use  gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).
 
|-
 
|-
−
|[https://github.com/broadinstitute/pilon/wiki pilon]
+
|[https://github.com/soedinglab/plass plass]
−
|1.21, 1.22
+
|2-c7e35-IGB-gcc-4.9.4<br>3-764a3
−
|Pilon is a software tool which can be used to: Automatically improve draft assemblies and Find variation among strains, including large event detection
+
|Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.
 
|-
 
|-
−
|[http://platanus.bio.titech.ac.jp/platanus-assembler/platanus-1-2-1/ platanus]
+
|[https://plastid.readthedocs.io/en/latest/ plastid]
−
|1.2.1
+
|0.5.1-IGB-gcc-8.2.0-Python-3.7.2
−
|Platanus: PLATform for Assembling NUcleotide Sequences
+
|plastid is a Python library for genomics and sequencing. It includes tools for exploratory data analysis (EDA) as well as a handful of scripts that implement common tasks.
 +
|-
 +
|[http://platanus.bio.titech.ac.jp/platanus-assembler platanus]
 +
|1.2.4
 +
|Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences ofhighly heterozygous diploids from massively parallel shotgun sequencing data.
 +
|-
 +
|[https://github.com/andyrimmer/Platypus Platypus]
 +
|20180622-IGB-gcc-4.9.4-Python-2.7.13
 +
|The Platypus variant caller.
 
|-
 
|-
 
|[https://www.cog-genomics.org/plink2 plink]
 
|[https://www.cog-genomics.org/plink2 plink]
−
|1.90beta3, 1.90beta
+
|1.07<br>1.90
−
|This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others.
+
|This is a comprehensive update to Shaun Purcells PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDKs Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others.  
 +
|-
 +
|[https://github.com/schneebergerlab/plotsr plotsr]
 +
|1.1.1-IGB-gcc-8.2.0-Python-3.10.1
 +
|Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies.
 +
|-
 +
|[https://github.com/nanoporetech/pomoxis pomoxis]
 +
|0.1.0-IGB-gcc-4.9.4-Python-3.6.1
 +
|Pomoxis contains a set of services to perform analysis of squiggles as they are produced in real-time along with fast pipelines for generating draft assemblies.
 +
|-
 +
|[https://github.com/bkehr/popins popins]
 +
|1.0.1-IGB-gcc-8.2.0
 +
|Population-scale detection of novel-sequence insertions.
 +
|-
 +
|[https://github.com/kehrlab/PopIns2 popins2]
 +
|20220127-IGB-gcc-8.2.0
 +
|Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
 
|-
 
|-
−
|[http://poamsa.sourceforge.net/ poa]
+
|[https://sourceforge.net/p/popoolation2/wiki/Main/ popoolation2]
−
|2.0
+
|1201-IGB-gcc-8.2.0-Perl-5.28.1
−
|POA is Partial Order Alignment, a fast program for multiple sequence alignment in bioinformatics. Its advantages are speed, scalability, sensitivity, and the superior ability to handle branching / indels in the alignment.
+
|PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences.
 +
|-
 +
|poppler
 +
|
 +
|Poppler is a PDF rendering library based on the xpdf-3.0 code base.
 +
|-
 +
|[https://github.com/statgen/popscle popscle]
 +
|20210504-IGB-gcc-8.2.0
 +
|popscle is a suite of population scale analysis tools for single-cell genomics data. The key software tools in this repository includes demuxlet (version 2) and freemuxlet, a genotyping-free method to deconvolute barcoded cells by their identities while detecting doublets.
 
|-
 
|-
−
|[http://genetics.bwh.harvard.edu/pph2/ polyphen]
+
|[https://github.com/rrwick/Porechop Porechop]
−
|2.2.2
+
|0.2.3-IGB-gcc-4.9.4-Python-3.6.1
−
|PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.
+
|Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.
 
|-
 
|-
 
|[https://github.com/arq5x/poretools poretools]
 
|[https://github.com/arq5x/poretools poretools]
−
|0.5.1, 0.6.0
+
|0.6.0-IGB-gcc-4.9.4-Python-2.7.13
 
|a toolkit for working with nanopore sequencing data from Oxford Nanopore.
 
|a toolkit for working with nanopore sequencing data from Oxford Nanopore.
 +
|-
 +
|[https://github.com/biobakery/biobakery/wiki/ppanini ppanini]
 +
|0.7.3.1-IGB-gcc-4.9.4-Python-2.7.13
 +
|PPANINI (Prioritization and Prediction of functional Annotation for Novel and Important genes via automated data Network Integration) is a computational pipeline that ranks genes by employing a combination of community parameters such as prevalence and abundance across samples.
 
|-
 
|-
 
|[http://matsen.fhcrc.org/pplacer/ pplacer]
 
|[http://matsen.fhcrc.org/pplacer/ pplacer]
−
|1.0, 1.1
+
|1.1.alpha19<br>1.1.alpha19-IGB-gcc-8.2.0-Python-3.7.2
 
|Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
 
|Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
 
|-
 
|-
−
|[http://wasabiapp.org/software/prank/ prank]
+
|[http://wasabiapp.org/software/prank/ PRANK]
−
|121002, 150803
+
|170427-IGB-gcc-4.9.4
 
|PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It’s based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.
 
|PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It’s based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.
 +
|-
 +
|[http://smithlabresearch.org/software/preseq/ preseq]
 +
|2.0.3-IGB-gcc-4.9.4<br>3.1.2-IGB-gcc-8.2.0
 +
|The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment.
 +
|-
 +
|[http://www.primer3.org primer3]
 +
|2.4.0-IGB-gcc-4.9.4
 +
|Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
 
|-
 
|-
 
|[http://prinseq.sourceforge.net/ prinseq]
 
|[http://prinseq.sourceforge.net/ prinseq]
−
|0.20.4
+
|0.20.4-IGB-gcc-4.9.4-Perl-5.24.1
−
|PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. It generates summary statistics of your sequences in graphical and tabular format. It is easily configurable and provides a user-friendly interface.
+
|PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data.  
 +
|-
 +
|[https://github.com/hyattpd/prodigal Prodigal]
 +
|2.6.3
 +
|Fast, reliable protein-coding gene prediction for prokaryotic genomes.
 +
|-
 +
|PROJ
 +
|
 +
|Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
 
|-
 
|-
−
|[http://prodigal.ornl.gov/ prodigal]
+
|[https://github.com/tseemann/prokka prokka]
−
|2.0, 2.2, 2.6.2
+
|1.13-IGB-gcc-4.9.4-Perl-5.24.1<br>1.14.6-IGB-gcc-4.9.4-Perl-5.24.1<br>1.14.6-IGB-gcc-8.2.0-Perl-5.28.1
−
|Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee
+
|Whole genome annotation is the process of identifying features of interest in a set of genomic DNA sequences, and labelling them with useful information. Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.
 
|-
 
|-
−
|[http://trac.osgeo.org/proj/ proj]
+
|[https://github.com/uoregon-postlethwait/prost Prost]
−
|4.8.0
+
|0.7.45-IGB-gcc-4.9.4-Python-2.7.13
−
|Program proj (release 3) is a standard Unix filter function which converts ge-ographic longitude and latitude coordinates into cartesian coordinates, (λ,φ)→(x,y), by means of a wide variety of cartographic projection functions.
+
|Prost (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembls BioMart, other databases, or may be custom built by the user).
 
|-
 
|-
−
|[http://www.bioinformatics.net.au/software.prokka.shtml prokka]
+
|[https://github.com/google-research/proteinfer proteinfer]
−
|1.10
+
|20220411-IGB-gcc-4.9.4-Python-3.6.1
−
|Prokka is a software tool for the rapid annotation of prokaryotic genomes. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA.
+
|ProteInfer is an approach for predicting the functional properties of protein sequences using deep neural networks.
 
|-
 
|-
−
|[http://pythonhosted.org/pyDNase/ pydnase]
+
|[https://github.com/gatech-genemark/ProtHint ProtHint]
−
|0.1.7
+
|2.5.0-IGB-gcc-8.2.0<br>2.6.0-IGB-gcc-8.2.0
−
|a library for analyzing DNase-seq data
+
|ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.
 +
|-
 +
|[https://github.com/google/protobuf protobuf]
 +
|2.6.1-IGB-gcc-4.9.4<br>23.4-IGB-gcc-8.2.0<br>3.5.0-IGB-gcc-4.9.4
 +
|Protocol Buffers (a.k.a., protobuf) are Googles language-neutral, platform-neutral, extensible mechanism for serializing structured data.
 +
|-
 +
|[https://github.com/google/protobuf/ protobuf-python]
 +
|3.19.4-IGB-gcc-8.2.0
 +
|Python Protocol Buffers runtime library.
 +
|-
 +
|[https://github.com/ddarriba/prottest3 prottest3]
 +
|3.4.2
 +
|ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT).
 +
|-
 +
|[https://github.com/psipred/psipred psipred]
 +
|4.0-IGB-gcc-8.2.0<br>4.02-IGB-gcc-8.2.0
 +
|The PSIPRED Workbench provides a range of protein structure prediction methods. The site can be used interactively via a web browser or programmatically via our REST API. For high-throughput analyses, downloads of all the algorithms are available.
 +
|-
 +
|[https://github.com/lilydjwg/pssh pssh]
 +
|2.3.1-IGB-gcc-4.9.4-Python-2.7.13
 +
|PSSH provides parallel versions of OpenSSH and related tools, including pssh, pscp, prsync, pnuke and pslurp. This project includes psshlib which can be used within custom applications.
 +
|-
 +
|[https://github.com/bcthomas/pullseq pullseq]
 +
|1.0.2-IGB-gcc-4.9.4
 +
|Utility program for extracting sequences from a fasta/fastq file
 +
|-
 +
|[https://github.com/dfguan/purge_dups purge_dups]
 +
|1.0.1-IGB-gcc-8.2.0-Python-3.7.2<br>1.2.5-IGB-gcc-8.2.0-Python-3.7.2
 +
|purge haplotigs and overlaps in an assembly based on read depth
 +
|-
 +
|[https://bitbucket.org/mroachawri/purge_haplotigs purge_haplotigs]
 +
|1.1.1-IGB-gcc-8.2.0
 +
|A simple pipeline for reassigning primary contigs that should be labelled as haplotigs.
 +
|-
 +
|[https://github.com/cytoscape/py2cytoscape py2cytoscape]
 +
|0.7.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|py2cytoscape is a collection of utilities to use Cytoscape and Cytoscape.js from Python. Network visualization feature is still limited in Python, but with this tool, you can access both of Cytoscape and Cytoscape.js as network visualization engines for your Python code!
 +
|-
 +
|[https://github.com/widdowquinn/pyani pyani]
 +
|0.2.10-IGB-gcc-4.9.4-Python-3.6.1
 +
|Python module for average nucleotide identity analyses
 +
|-
 +
|[https://daler.github.io/pybedtools/main.html pybedtools]
 +
|0.7.10-IGB-gcc-4.9.4-Python-3.6.1<br>0.8.2-IGB-gcc-8.2.0-Python-3.7.2<br>0.9.0-IGB-gcc-8.2.0-Python-3.7.2
 +
|pybedtools is a Python package that wraps BEDTools, so you will need both installed.
 +
|-
 +
|[https://pybind11.readthedocs.io pybind11]
 +
|2.9.2-IGB-gcc-8.2.0
 +
|pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.
 +
|-
 +
|[https://pycairo.readthedocs.io/en/latest/ pycairo]
 +
|1.19.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|Pycairo is a Python module providing bindings for the cairo graphics library. It depends on cairo >= 1.15.10 and works with Python 3.7+. Pycairo, including this documentation, is licensed under the LGPL-2.1-only OR MPL-1.1.
 +
|-
 +
|[https://mathema.tician.de/software/pycuda/ PyCUDA]
 +
|2017.1-IGB-gcc-4.9.4-Python-2.7.13
 +
|PyCUDA lets you access Nvidia‘s CUDA parallel computation API from Python. - Homepage: https://mathema.tician.de/software/pycuda/
 +
|-
 +
|[https://mathema.tician.de/software/pycuda/ pyCUDA]
 +
|2024.1-IGB-gcc-8.2.0-Python-3.10.1
 +
|PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python. Several wrappers of the CUDA API already exist-so what’s so special about PyCUDA?
 
|-
 
|-
 
|[https://github.com/brentp/pyfasta/ pyfasta]
 
|[https://github.com/brentp/pyfasta/ pyfasta]
−
|0.5.2
+
|0.5.2-IGB-gcc-4.9.4-Python-2.7.13
−
|Stores a flattened version of the fasta file without spaces or headers and uses either a mmap of numpy binary format or fseek/fread so the sequence data is never read into memory. Saves a pickle (.gdx) of the start, stop (for fseek/mmap) locations of each header in the fasta file for internal use.
+
|Stores a flattened version of the fasta file without spaces or headers and uses either a mmap of numpy binary format or fseek/fread so the sequence data is never read into memory.
 
|-
 
|-
−
|[https://pypi.python.org/pypi/pyfftw pyfftw]
+
|[https://github.com/deeptools/pyGenomeTracks pyGenomeTracks]
−
|0.10.4
+
|3.8-IGB-gcc-8.2.0-Python-3.7.2
−
|pyFFTW is a pythonic wrapper around FFTW 3, the speedy FFT library. The ultimate aim is to present a unified interface for all the possible transforms that FFTW can perform.
+
|pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable.
 
|-
 
|-
−
|[http://pygraphviz.github.io/ pygraphviz]
+
|[http://deeplearning.net/software/libgpuarray pygpu]
−
|1.3rc1
+
|0.6.5-IGB-gcc-4.9.4-Python-2.7.13
 +
|Python bindings for libgpuarray - Homepage: http://deeplearning.net/software/libgpuarray
 +
|-
 +
|[https://pygraphviz.github.io/ pygraphviz]
 +
|1.3.1-IGB-gcc-4.9.4-Python-3.6.1
 
|PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms.
 
|PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms.
 
|-
 
|-
−
|[http://deeplearning.net/software/pylearn2/ pylearn2]
+
|[https://github.com/lisa-lab/pylearn2 pylearn2]
−
|201601
+
|20170525-IGB-gcc-4.9.4-Python-2.7.13
−
|Pylearn2 is a machine learning library. Most of its functionality is built on top of Theano.
+
|Pylearn2 is a library designed to make machine learning research easy. - Homepage: https://github.com/lisa-lab/pylearn2
 +
|-
 +
|[https://pymol.org/2/ pymol]
 +
|2.3.4
 +
|PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
 +
|-
 +
|[https://www.pypy.org pypy]
 +
|7.3.5-IGB-gcc-4.9.4-Python-2.7.13
 +
|A fast, compliant alternative implementation of Python
 +
|-
 +
|[http://www.pyrosetta.org/ PyRosetta]
 +
|2021.25-IGB-gcc-8.2.0-Python-3.7.2
 +
|PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
 
|-
 
|-
−
|[http://pypy.org/ pypy]
+
|[http://python.org/ Python]
−
|4.0.1
+
|2.7.13-IGB-gcc-4.9.4<br>2.7.18-IGB-gcc-8.2.0<br>3.10.1-IGB-gcc-8.2.0<br>3.6.1-IGB-gcc-4.9.4<br>3.7.2-IGB-gcc-8.2.0
−
|PyPy is a fast, compliant alternative implementation of the Python language (2.7.10 and 3.2.5). It has several advantages and distinct features:
+
|Python is a programming language that lets you work more quickly and integrate your systems more effectively.
 
|-
 
|-
−
|[http://pyqt.sourceforge.net/ pyqt]
+
|[http://pytorch.org PyTorch]
−
|4.11.2
+
|0.3.0-IGB-gcc-4.9.4-Python-3.6.1<br>0.4.0-IGB-gcc-4.9.4-Python-3.6.1<br>0.4.1-IGB-gcc-4.9.4-Python-2.7.13<br>1.0.1.post2-IGB-gcc-4.9.4-Python-3.6.1<br>1.11.0-IGB-gcc-8.2.0-Python-3.7.2<br>1.12.1-IGB-gcc-8.2.0-Python-3.10.1<br>1.12.1-IGB-gcc-8.2.0-Python-3.7.2<br>1.13.1-IGB-gcc-8.2.0-Python-3.7.2<br>1.3.1-IGB-gcc-4.9.4-Python-3.6.1<br>1.4.0-IGB-gcc-4.9.4-Python-3.6.1<br>1.6.0-IGB-gcc-4.9.4-Python-3.6.1<br>1.7.0-IGB-gcc-8.2.0-Python-3.7.2<br>1.9.0-IGB-gcc-8.2.0-Python-3.7.2
−
|PyQt is the Python bindings for Digia's Qt cross-platform application development framework.
+
|Tensors and Dynamic neural networks in Pythonwith strong GPU acceleration.
 
|-
 
|-
−
|[http://dereneaton.com/software/pyrad/ pyrad]
+
|[https://github.com/pyg-team/pytorch_geometric pytorch-geometric]
−
|3.0.66
+
|2.0.4-IGB-gcc-8.2.0-Python-3.7.2
−
|The benefit of pyRAD over most alternative methods for analyzing RADseq-like data comes in its use of an alignment-clustering method (vsearch) that allows for the inclusion of indel variation which improves identification of homology across highly divergent samples. For this reason pyRAD is commonly employed for RADseq studies at deeper phylogenetic scales, however, it works equally well at shallow scales.
+
|PyG (PyTorch Geometric) is a library built upon PyTorch to easily write and train Graph Neural Networks (GNNs) for a wide range of applications related to structured data.
 
|-
 
|-
−
|[https://pypi.python.org/pypi/pysam pysam]
+
|[http://www.zeromq.org/bindings:python PyZMQ]
−
|0.8.0, 0.8.4, 0.9.1.4
+
|16.0.2-IGB-gcc-4.9.4-Python-3.6.1
−
|Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API
+
|Python bindings for ZeroMQ
 
|-
 
|-
−
|[https://www.python.org/ python]
+
|[https://github.com/freezer333/qgrs-cpp qgrs]
−
|2.6.6, 2.7.3, 2.7.6, 2.7.9, 3.4.1
+
|1.0-IGB-gcc-4.9.4
−
|Python is a programming language that lets you work quickly and integrate systems more effectively.
+
|C++ implementation of QGRS mapping algorithm - described here. This program differs from the actual algorithm used by QGRS Mapper recarding overlapping motifs and the maximum length of the motif.
 
|-
 
|-
−
|[http://qiime.org/ qiime]
+
|[http://qiime.org/ QIIME]
−
|1.3.0, 1.5.0, 1.6.0, 1.7.0, 1.8, 1.9.0, 1.9.1
+
|1.9.1
−
|QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QIIME is designed to take users from raw sequencing data generated on the Illumina or other platforms through publication quality graphics and statistics. This includes demultiplexing and quality filtering, OTU picking, taxonomic assignment, and phylogenetic reconstruction, and diversity analyses and visualizations. QIIME has been applied to studies based on billions of sequences from tens of thousands of samples.
+
|QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
 
|-
 
|-
−
|[http://qt-project.org/ qt]
+
|[http://qiime.org/ QIIME2]
−
|4.8.6
+
|2017.10<br>2017.11<br>2017.12<br>2017.6<br>2017.8<br>2018.11<br>2018.2<br>2018.6<br>2018.8<br>2019.10<br>2019.4<br>2019.7<br>2020.2<br>2020.6<br>2020.8<br>2021.4<br>2022.8<br>2023.2<br>2023.7
−
|Qt is a cross-platform application and UI framework for developers using C++ or QML, a CSS & JavaScript like language
+
|QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
 
|-
 
|-
−
|[http://www.cbcb.umd.edu/software/quake/ quake]
+
|[http://qt.io/ Qt]
−
|0.3.4
+
|4.8.7-IGB-gcc-4.9.4<br>4.8.7-IGB-gcc-8.2.0
−
|Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
+
|Qt is a comprehensive cross-platform C++ application framework.
 
|-
 
|-
−
|[http://bioinf.spbau.ru/quast quast]
+
|[http://qualimap.bioinfo.cipf.es/ qualimap]
−
|2.2, 2.3
+
|2.2.1-Java-1.8.0_121
−
|QUAST evaluates genome assemblies.  It can works both with and without a given reference genome.  The tool accepts multiple assemblies, thus is suitable for comparison.
+
|Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.  
 
|-
 
|-
−
|quest
+
|[https://sourceforge.net/projects/quast/ quast]
−
|alpha, devel
+
|4.6.1-IGB-gcc-4.9.4-Python-2.7.13<br>5.0.0-IGB-gcc-4.9.4-Python-3.6.1<br>5.0.2-IGB-gcc-8.2.0-Python-3.7.2
−
|adds environmental variables for EFI QUEST development branch
+
|QUAST performs fast and convenient quality evaluation and comparison of genome assemblies.
 +
|-
 +
|[https://github.com/mahulchak/quickmerge quickmerge]
 +
|0.2-IGB-gcc-4.9.4-Python-2.7.13
 +
|quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve contiguities of an assembly generated with PacBio long reads alone. This is counterintuitive because illumina short reads are not typically considered to cover genomic regions which PacBio long reads cannot. Although we have not evaluated this program for assemblies generated with Oxford nanopore sequences, the program should work with ONP-assemblies too.
 
|-
 
|-
 
|[http://www.r-project.org/ R]
 
|[http://www.r-project.org/ R]
−
|2.15.0, 2.15.1, 2.15.2, 2.15.3, 3.0.0, 3.0.2, 3.1.0, 3.1.1, 3.1.2, 3.2.0, 3.2.3, 3.3.3, experimental
+
|2.15.3-IGB-gcc-4.9.4<br>3.1.2-IGB-gcc-4.9.4<br>3.2.5-IGB-gcc-4.9.4<br>3.3.3-IGB-gcc-4.9.4<br>3.4.1-IGB-gcc-4.9.4<br>3.4.2-IGB-gcc-4.9.4<br>3.5.0-IGB-gcc-4.9.4<br>3.6.0-IGB-gcc-8.2.0<br>4.0.3-IGB-gcc-8.2.0<br>4.1.2-IGB-gcc-8.2.0<br>4.2.2-IGB-gcc-8.2.0<br>4.3.2-IGB-gcc-8.2.0
 
|R is a free software environment for statistical computing and graphics.
 
|R is a free software environment for statistical computing and graphics.
 
|-
 
|-
−
|[http://bioen-compbio.bioen.illinois.edu/RACA/ RACA]
+
|[https://github.com/isovic/racon racon]
−
|0.9.1.1
+
|0.5.0-IGB-gcc-4.9.4-Python-2.7.13<br>0.5.0-IGB-gcc-4.9.4-Python-3.6.1<br>1.4.13-IGB-gcc-8.2.0
−
|Reference-Assisted Chromosome Assembly
+
|Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step, such as Miniasm.The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods.
 
|-
 
|-
−
|[https://github.com/johnomics/RADtools radtools]
+
|[https://github.com/AndreasHeger/radar radar]
−
|1.2.4
+
|1.3-IGB-gcc-8.2.0
−
|Tools for processing RAD Sequencing Illumina reads.
+
|Welcome to radar
 +
|-
 +
|[http://catchenlab.life.illinois.edu/radinitio/ radinitio]
 +
|1.1.0-IGB-gcc-4.9.4-Python-3.6.1<br>1.1.1-IGB-gcc-4.9.4-Python-3.6.1
 +
|RADinitio is a simulation pipeline for the assessment of RADseq experiments. Genetic data are forward simulated for a population of individuals from a designated reference genome.
 +
|-
 +
|[http://fenderglass.github.io/Ragout/ Ragout]
 +
|2.0-IGB-gcc-4.9.4
 +
|Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references.
 +
|-
 +
|[https://github.com/malonge/RagTag RagTag]
 +
|1.0.2-IGB-gcc-8.2.0-Python-3.7.2<br>1.1.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|RagTag, the successor to RaGOO, is a command line tool for reference-guided genome assembly improvement.
 +
|-
 +
|[https://github.com/bcgsc/RAILS RAILS]
 +
|1.5.1-IGB-gcc-8.2.0
 +
|RAILS and Cobbler are genomics application for scaffolding and automated finishing of genome assemblies with long DNA sequences. They can be used to scaffold & finish high-quality draft genome assemblies with any long, preferably high-quality, sequences such as scaftigs/contigs from another genome draft.
 +
|-
 +
|[http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/ randfold]
 +
|2.0.1-IGB-gcc-4.9.4
 +
|Minimum free energy of folding randomization test software
 +
|-
 +
|[https://github.com/stamatak/standard-RAxML RAxML]
 +
|8.2.12-IGB-gcc-4.9.4
 +
|RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
 +
|-
 +
|[https://github.com/amkozlov/raxml-ng raxml-ng]
 +
|1.2.0
 +
|RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.
 +
|-
 +
|[https://rclone.org/ rclone]
 +
|1.41<br>1.52.3<br>1.60.0
 +
|Rclone is a command line program to sync files and directories to and from different cloud storage
 +
|-
 +
|[https://cran.r-project.org/web/packages/RcppGSL/index.html RcppGSL]
 +
|0.3.2-IGB-gcc-4.9.4-R-3.3.3
 +
|Rcpp integration for GNU GSL vectors and matrices The GNU Scientific Library (or GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp which is itself a package that eases the interfaces between R and C++. This package also serves as a prime example of how to build a package that uses Rcpp to connect to another third-party library. The autoconf script, inline plugin and example package can all be used as a stanza to write a similar package against another library.
 +
|-
 +
|[https://github.com/rdkit/rdkit rdkit]
 +
|2020_03_3-IGB-gcc-4.9.4-Python-3.6.1<br>2021_03_1-IGB-gcc-8.2.0-Python-3.7.2
 +
|RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
 +
|-
 +
|[https://sourceforge.net/projects/rdp-classifier RDPClassifier]
 +
|2.12-Java-1.8.0_152<br>2.2-Java-1.8.0_152
 +
|The RDP Classifier is a naive Bayesian classifier which was developed to provide rapid taxonomic placement based on rRNA sequence data. The RDP Classifier can rapidly and accurately classify bacterial and archaeal 16s rRNA sequences, and Fungal LSU sequences. It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
 +
|-
 +
|[https://reademption.readthedocs.io/en/latest/ READemption]
 +
|1.0.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 (Pubmed)) originating from bacterial samples.
 
|-
 
|-
−
|[http://fenderglass.github.io/Ragout/ ragout]
+
|[https://faculty.washington.edu/tathornt/software/REAP/index.html REAP]
−
|2.0
+
|1.2-IGB-gcc-8.2.0
−
|Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references. Given a set of assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds).
+
|
 
|-
 
|-
−
|[https://github.com/zhaoyanswill/RAPSearch2 rapsearch2]
+
|[http://www.sanger.ac.uk/science/tools/reapr REAPR]
−
|2.22
+
|1.0.18-IGB-gcc-4.9.4
−
|Reduced Alphabet based Protein similarity Search
+
|REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls. - Homepage: http://www.sanger.ac.uk/science/tools/reapr
 
|-
 
|-
−
|[http://sco.h-its.org/exelixis/software.html RAxML]
+
|[http://eddylab.org/software/recon/ RECON]
−
|7.3.0
+
|1.08-IGB-gcc-4.9.4-Perl-5.24.1
−
|RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.
+
|a package for automated de novo identification of repeat families from genomic sequences
 
|-
 
|-
−
|[http://denovoassembler.sourceforge.net/index.html ray]
+
|[https://github.com/biocore/redbiom redbiom]
−
|2.20, 2.30
+
|0.3.2-IGB-gcc-4.9.4-Python-3.6.1
−
|Ray -- Parallel genome assemblies for parallel DNA sequencing
+
|Redbiom is a cache service for sample metadata and sample data.
 
|-
 
|-
−
|[https://github.com/mourisl/Rcorrector/ Rcorrector]
+
|[http://www.repeatmasker.org/ RepeatMasker]
−
|1.0.1
+
|4.0.7-IGB-gcc-4.9.4-Perl-5.24.1<br>4.0.7-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded<br>4.1.1-IGB-gcc-4.9.4-Perl-5.24.1<br>4.1.2-p1-IGB-gcc-8.2.0-Perl-5.28.1
−
|Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data.
+
|RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.  
 
|-
 
|-
−
|[http://rdp.cme.msu.edu/ rdp_classifier]
+
|[http://www.repeatmasker.org/RepeatModeler/ RepeatModeler]
−
|2.5
+
|1.0.11-IGB-gcc-4.9.4-Perl-5.24.1<br>2.0.1-IGB-gcc-4.9.4-Perl-5.24.1<br>2.0.2a-IGB-gcc-4.9.4-Perl-5.24.1
−
|The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
+
|RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.
 
|-
 
|-
−
|[http://rdxplorer.sourceforge.net/ rdxplorer]
+
|[http://www.repeatmasker.org/RepeatModeler/ RepeatScout]
−
|3.2
+
|1.0.5-IGB-gcc-4.9.4
−
|The RDXplorer (Read Depth eXplorer) is a computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. CNV detection is based on the Event-Wise Testing (EWT) algorithm recently published by our group (see Publications). The read depth coverage is estimated in non-overlapping intervals (100bp Windows) across an individual genome based on the pileup generated by SAMTools.
+
|De Novo Repeat Finder,
 
|-
 
|-
−
|[http://www.repeatmasker.org/ repeatmasker]
+
|[https://github.com/jasperlinthorst/reveal reveal]
−
|3.28, 4.0.5
+
|0.2.2-IGB-gcc-4.9.4-Python-2.7.13
−
|RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences
+
|REVEAL (REcursiVe Exact-matching ALigner) can be used to (multi) align whole genomes.
 
|-
 
|-
−
|[https://sites.google.com/site/rfmixlocalancestryinference/ RFMix]
+
|[https://github.com/slowkoni/rfmix RFMix]
−
|1.5.4
+
|20180503-IGB-gcc-4.9.4
 
|A discriminative method for local ancestry inference
 
|A discriminative method for local ancestry inference
 +
|-
 +
|[https://cran.r-project.org/web/packages/rgeos/index.html rgeos]
 +
|0.4-2-IGB-gcc-4.9.4-R-3.5.0
 +
|nterface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries.
 +
|-
 +
|[http://www.regulatory-genomics.org/rgt/basic-introduction/ RGT]
 +
|0.11.3-IGB-gcc-4.9.4-Python-2.7.13
 +
|Regulatory Genomics Toolbox (RGT) is an open source python library for analysis of regulatory genomics. RGT is programmed in an oriented object fashion and its core classes provide functionality for handling regulatory genomics data.
 
|-
 
|-
 
|[http://rnaseq-mats.sourceforge.net/ rMATS]
 
|[http://rnaseq-mats.sourceforge.net/ rMATS]
−
|3.0.9
+
|3.2.5-IGB-gcc-4.9.4-Python-2.7.13
−
|MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold.
+
|MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.
 +
|-
 +
|[https://github.com/Xinglab/rmats-turbo rMATS-turbo]
 +
|4.1.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net).
 +
|-
 +
|[http://www.repeatmasker.org/RMBlast.html RMBlast]
 +
|2.11.0-IGB-gcc-8.2.0<br>2.6.0-IGB-gcc-4.9.4<br>2.9.0-IGB-gcc-4.9.4
 +
|RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.
 +
|-
 +
|[https://cran.r-project.org/web/packages/Rmpi/index.html Rmpi]
 +
|0.6-6-IGB-gcc-4.9.4-R-3.4.2
 +
|An interface (wrapper) to MPI APIs. It also provides interactive R manager and worker environment.
 +
|-
 +
|[https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid RNAhybrid]
 +
|2.1.2-IGB-gcc-4.9.4
 +
|RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.
 +
|-
 +
|[http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer RNAmmer]
 +
|1.2-IGB-gcc-4.9.4-Perl-5.24.1<br>1.2-IGB-gcc-8.2.0-Perl-5.28.1
 +
|Ribosomal RNA sub units
 +
|-
 +
|[https://github.com/ablab/rnaquast rnaquast]
 +
|2.1.0-IGB-gcc-8.2.0-Python-3.7.2
 +
|rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
 
|-
 
|-
−
|rnaQUAST
+
|[https://github.com/Kingsford-Group/rnaseqtools rnaseqtools]
−
|1.1.0
+
|1.0.2-IGB-gcc-4.9.4
−
|Homepage:
+
|This repo rnaseqtools provides a set of tools to process transcripts (mainly in gtf format).
 +
|-
 +
|[http://rna.urmc.rochester.edu/RNAstructure.html RNAstructure]
 +
|6.0-IGB-gcc-4.9.4
 +
|RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities.
 +
|-
 +
|[https://sanger-pathogens.github.io/Roary/ roary]
 +
|3.13.0-IGB-gcc-4.9.4-Perl-5.24.1
 +
|Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.
 
|-
 
|-
−
|[http://cs.wellesley.edu/~btjaden/Rockhopper/ rockhopper]
+
|[https://www.ripp.rodeo/index.html rodeo2]
−
|1.2, 2.0.2
+
|2.4.2-IGB-gcc-8.2.0-Python-3.7.2
−
|Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data. As input, Rockhopper takes RNA sequencing reads output by high-throughput sequencing technology (FASTQ, QSEQ, FASTA, SAM, or BAM files)
+
|RODEO evaluates one or many genes, characterizing a gene neighborhood based on the presence of profile hidden Markov models (pHMMs).
 
|-
 
|-
 
|[https://root.cern.ch/ root]
 
|[https://root.cern.ch/ root]
−
|6.06
+
|6.14.06-IGB-gcc-4.9.4<br>6.14.06-IGB-gcc-4.9.4-Python-2.7.13
−
|A modular scientific software framework. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage.
+
|A modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R.
 
|-
 
|-
−
|[http://www.rsat.eu/ rsa-tools]
+
|[https://github.com/Abe404/root_painter root-painter-trainer]
−
|2012-10-09
+
|0.2.19.1-IGB-gcc-8.2.0-Python-3.10.1
−
|RSAT: Regulatory Sequence Analysis Tools
+
|RootPainter is a GUI-based software tool for the rapid training of deep neural networks for use in biological image analysis. RootPainter uses a client-server architecture, allowing users with a typical laptop to utilise a GPU on a more computationally powerful server.
 +
|-
 +
|[http://younglab.wi.mit.edu/super_enhancer_code.html ROSE]
 +
|20150210-IGB-gcc-4.9.4-Python-2.7.13
 +
|To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam)
 +
|-
 +
|[https://www.rosettacommons.org/ rosetta]
 +
|2017.52-IGB-gcc-4.9.4<br>3.12-IGB-gcc-4.9.4<br>3.13-IGB-gcc-8.2.0
 +
|The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.
 +
|-
 +
|[http://rpy.sourceforge.net/ rpy]
 +
|1.0.3-IGB-gcc-4.9.4-Python-2.7.13-R-2.15.3
 +
|RPy is a very simple, yet robust, Python interface to the R Programming Language. Itcan manage all kinds of R objects and can execute arbitrary R functionsincluding the graphic functions.
 +
|-
 +
|[http://rpy.sourceforge.net/ rpy2]
 +
|2.8.6-IGB-gcc-4.9.4-Python-2.7.13-R-3.3.3<br>2.8.6-IGB-gcc-4.9.4-Python-2.7.13-R-3.5.0<br>2.9.0-IGB-gcc-4.9.4-Python-3.6.1-R-3.3.3<br>2.9.5-IGB-gcc-8.2.0-Python-3.7.2-R-4.1.2<br>3.0.1-IGB-gcc-4.9.4-Python-3.6.1-R-3.5.0<br>3.2.4-IGB-gcc-8.2.0-Python-3.7.2-R-3.6.0<br>3.4.5-IGB-gcc-8.2.0-Python-3.7.2-R-4.1.2
 +
|rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.
 +
|-
 +
|[https://github.com/Alexamk/RREFinder RREFinder]
 +
|1.0.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|Bioinformatic application for the detection of RREs in protein sequences of interest
 +
|-
 +
|[https://github.com/rsa-tools/rsat-code RSAT]
 +
|20230828-IGB-gcc-8.2.0
 +
|We offer tools to analyse cis-regulatory elements in genome sequences, motif discovery (support genome-wide data sets like ChIP-seq), transcription factor binding motif analysis (quality assessment, comparisons and clustering), comparative genomics, analysis of regulatory variations
 
|-
 
|-
 
|[http://deweylab.github.io/RSEM/ RSEM]
 
|[http://deweylab.github.io/RSEM/ RSEM]
−
|1.2.29, 1.2.31
+
|1.3.0-IGB-gcc-4.9.4<br>1.3.1-IGB-gcc-4.9.4<br>1.3.3-IGB-gcc-8.2.0
−
|RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. The RSEM package provides an user-friendly interface, supports threads for parallel computation of the EM algorithm, single-end and paired-end read data, quality scores, variable-length reads and RSPD estimation.
+
|RNA-Seq by Expectation-Maximization
 
|-
 
|-
−
|[http://www.rstudio.com/ rstudio]
+
|[http://rseqc.sourceforge.net/ RSeQC]
−
|0.97.312, 0.98.1102
+
|2.6.4-IGB-gcc-4.9.4-Python-2.7.13
−
|RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
+
|RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
 
|-
 
|-
−
|[http://realtimegenomics.com/products/rtg-tools/ rtg-tools]
+
|[https://posit.co/download/rstudio-desktop/ RStudio]
−
|3.6.2
+
|2023.09.1-494
 +
|Used by millions of people weekly, the RStudio integrated development environment (IDE) is a set of tools built to help you be more productive with R and Python.
 +
|-
 +
|[https://www.realtimegenomics.com/products/rtg-tools rtg-tools]
 +
|3.8.4
 
|RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats.
 
|RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats.
 
|-
 
|-
−
|[https://www.ruby-lang.org ruby]
+
|[https://www.ruby-lang.org Ruby]
−
|1.9.3, 2.3.1
+
|2.4.2-IGB-gcc-4.9.4
−
|Ruby is a language of careful balance. Its creator, Yukihiro “Matz” Matsumoto, blended parts of his favorite languages (Perl, Smalltalk, Eiffel, Ada, and Lisp) to form a new language that balanced functional programming with imperative programming.
+
|Ruby is a dynamic, open source programming language with  a focus on simplicity and productivity. It has an elegant syntax that is  natural to read and easy to write.
 +
|-
 +
|[https://www.rust-lang.org Rust]
 +
|1.41.1
 +
|Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
 +
|-
 +
|[https://github.com/najoshi/sabre sabre]
 +
|20171114-IGB-gcc-4.9.4
 +
|Next-generation sequencing can currently produce hundreds of millions of reads per lane of sample and that number increases at a dizzying rate. Barcoding individual sequences for multiple lines or multiple species is a cost-efficient method to sequence and analyze a broad range of data.
 
|-
 
|-
−
|[http://s3tools.org/s3cmd s3cmd]
+
|[https://github.com/XDynames/SAI-app SAI-app]
−
|1.5.2
+
|20230425-IGB-gcc-8.2.0-Python-3.7.2
−
|S3cmd is a free command line tool and client for uploading, retrieving and managing data in Amazon S3 and other cloud storage service providers that use the S3 protocol, such as Google Cloud Storage or DreamHost DreamObjects. It is best suited for power users who are familiar with command line programs. It is also ideal for batch scripts and automated backup to S3, triggered from cron, etc.
+
|StomaAI application
 
|-
 
|-
−
|[https://github.com/COMBINE-lab/salmon/ salmon]
+
|[https://github.com/COMBINE-lab/salmon Salmon]
−
|0.4.2, 0.6.0, 0.7.1, 0.7.2, 0.8.2
+
|0.11.3-IGB-gcc-4.9.4<br>0.12.0-IGB-gcc-8.2.0<br>0.13.1-IGB-gcc-8.2.0<br>0.14.1-IGB-gcc-8.2.0<br>0.8.2-IGB-gcc-4.9.4-Python-2.7.13<br>0.9.1-IGB-gcc-4.9.4<br>1.0.0-IGB-gcc-8.2.0<br>1.1.0-IGB-gcc-8.2.0<br>1.10.0-IGB-gcc-8.2.0<br>1.2.1-IGB-gcc-8.2.0<br>1.4.0-IGB-gcc-8.2.0<br>1.5.2-IGB-gcc-8.2.0
 
|Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
 
|Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
 
|-
 
|-
−
|[https://github.com/lomereiter/sambamba sambamba]
+
|[http://liuzlab.org/salmonte/ SalmonTE]
−
|0.6.3
+
|0.4-IGB-gcc-8.2.0
−
|Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.
+
|SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data.
 +
|-
 +
|[https://github.com/COMBINE-lab/SalmonTools SalmonTools]
 +
|20190604-IGB-gcc-8.2.0
 +
|Useful tools for working with Salmon output
 +
|-
 +
|[https://github.com/marbl/SALSA SALSA]
 +
|2.2-IGB-gcc-4.9.4-Python-2.7.13<br>2.3-IGB-gcc-4.9.4-Python-2.7.13
 +
|A tool to scaffold long read assemblies with Hi-C
 +
|-
 +
|[https://github.com/weiquan/salt salt]
 +
|beta0.2-IGB-gcc-8.2.0
 +
|alignment algorithm that is SNP-aware
 +
|-
 +
|[http://lomereiter.github.io/sambamba/ sambamba]
 +
|0.6.6<br>0.8.0
 +
|sambamba view allows to efficiently filter SAM/BAM/CRAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences.
 
|-
 
|-
 
|[https://github.com/GregoryFaust/samblaster samblaster]
 
|[https://github.com/GregoryFaust/samblaster samblaster]
−
|0.1.22
+
|0.1.24-IGB-gcc-4.9.4
−
|samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
+
|ummary samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
 
|-
 
|-
−
|[http://www.htslib.org/ samtools]
+
|[http://www.htslib.org/ SAMtools]
−
|0.1.16, 0.1.18, 0.1.19, 1.0, 1.2, 1.3.1
+
|0.1.18-IGB-gcc-4.9.4<br>0.1.20-IGB-gcc-4.9.4<br>0.1.20-IGB-gcc-8.2.0<br>1.10-IGB-gcc-8.2.0<br>1.11-IGB-gcc-8.2.0<br>1.12-IGB-gcc-8.2.0<br>1.17-IGB-gcc-8.2.0<br>1.3.1-IGB-gcc-4.9.4<br>1.4-IGB-gcc-4.9.4<br>1.4.1-IGB-gcc-4.9.4<br>1.5-IGB-gcc-4.9.4<br>1.7-IGB-gcc-4.9.4<br>1.9-IGB-gcc-4.9.4
−
|Samtools is a suite of programs for interacting with high-throughput sequencing data. It consists of three separate repositories
+
|SAM Tools provide various utilities for manipulating alignments in the SAM format,  including sorting, merging, indexing and generating alignments in a per-position format.
 
|-
 
|-
−
|[http://sourceforge.net/projects/samcomp/ sam_comp]
+
|[https://www.shorelinebiome.com/sbanalyzer-software/ sbanalyzer]
−
|0.7
+
|3.0-14<br>3.1-2
−
|This is a simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.
+
|Shoreline Biome’s unique microbiome kits are the key to generating long-read next-generation sequencing data necessary to discriminate microbial strains from any sample.  
 
|-
 
|-
−
|[http://edwards.sdsu.edu/scaffold_builder/ scaffold-builder]
+
|ScaLAPACK
−
|2.1
+
|
−
|The abundance of repeat elements in genomes can impede the assembly of a single sequence. The tool Scaffold_builder was designed to generate scaffolds (super contigs of sequences joined by N-bases) using the homology provided by a closely related reference sequence.
+
|The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
 +
|-
 +
|[https://github.com/Kingsford-Group/scallop scallop]
 +
|0.10.3-IGB-gcc-4.9.4<br>0.10.4-IGB-gcc-4.9.4
 +
|Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.
 +
|-
 +
|[https://github.com/lebedov/scikit-cuda scikit-cuda]
 +
|0.5.1-IGB-gcc-4.9.4-Python-2.7.13
 +
|scikit-cuda provides Python interfaces to many of the functions in the CUDA device/runtime, CUBLAS, CUFFT, and CUSOLVER libraries distributed as part of NVIDIAs CUDA Programming Toolkit, as well as interfaces to select functions in the free and standard versions of the CULA Dense Toolkit. Both low-level wrapper functions similar to their C counterparts and high-level functions comparable to those in NumPy and Scipy are provided.
 +
|-
 +
|[https://github.com/AdmiralenOla/Scoary scoary]
 +
|1.6.16-IGB-gcc-4.9.4-Python-3.6.1
 +
|Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. It reports a list of genes sorted by strength of association per trait.
 +
|-
 +
|[http://www.scons.org/ SCons]
 +
|3.0.1-IGB-gcc-4.9.4-Python-2.7.13<br>3.0.1-IGB-gcc-4.9.4-Python-3.6.1
 +
|SCons is a software construction tool.
 +
|-
 +
|[https://github.com/nanoporetech/scrappie scrappie]
 +
|1.3.0-IGB-gcc-4.9.4
 +
|Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group.
 +
|-
 +
|[http://www.libsdl.org/ SDL2]
 +
|2.0.4-IGB-gcc-4.9.4
 +
|SDL: Simple DirectMedia Layer, a cross-platform multimedia library
 +
|-
 +
|[https://www.bioinf.uni-leipzig.de/Software/segemehl segemehl]
 +
|0.3.4-IGB-gcc-8.2.0
 +
|segemehl is a software to map short sequencer reads to reference genomes. segemehl implements a matching strategy based on enhanced suffix arrays (ESA)
 +
|-
 +
|[https://www.pmgenomics.ca/hoffmanlab/proj/segway/ Segway]
 +
|2.0.1-IGB-gcc-4.9.4-Python-2.7.13
 +
|Segway is a tool for easy pattern discovery and identification in functional genomics data.
 +
|-
 +
|[https://www.sentieon.com/ sentieon]
 +
|201808<br>201911<br>202010.01<br>202112<br>202112.01<br>202112.04<br>202112.06<br>202308<br>202308.02
 +
|A fast and accurate solution to variant calling from next-generation sequence data
 +
|-
 +
|[https://github.com/smirarab/sepp SEPP]
 +
|20180223-IGB-gcc-4.9.4-Python-2.7.13<br>4.3.10-IGB-gcc-8.2.0-Python-3.7.2<br>4.5.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
 +
|-
 +
|[https://www.seqan.de/ seqan]
 +
|2.2.0-IGB-gcc-8.2.0<br>2.3.2-IGB-gcc-4.9.4
 +
|SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data
 +
|-
 +
|[https://bioinf.shenwei.me/seqkit seqkit]
 +
|0.12.1<br>0.15.0<br>2.0.0<br>2.3.0<br>2.5.1<br>2.6.1
 +
|a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
 +
|-
 +
|SeqLib
 +
|
 +
|C++ interface to HTSlib, BWA-MEM and Fermi
 
|-
 
|-
−
|[http://www.scipy.org/ scipy]
+
|[https://github.com/jstjohn/SeqPrep SeqPrep]
−
|0.15.1
+
|1.3.2-IGB-gcc-8.2.0
−
|Python-based ecosystem of open-source software for mathematics, science, and engineering.
+
|SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap.
 
|-
 
|-
−
|[http://www.scons.org/ scons]
+
|[https://github.com/lh3/seqtk/ seqtk]
−
|2.3.4
+
|1.2-IGB-gcc-4.9.4<br>1.2-IGB-gcc-8.2.0<br>1.3-IGB-gcc-8.2.0
−
|SCons is an Open Source software construction tool.that is, a next-generation build tool.
+
|Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
 
|-
 
|-
−
|[https://github.com/szpiech/selscan selscan]
+
|[https://github.com/ISUgenomics/SequelTools SequelTools]
−
|1.1.0
+
|20200619-IGB-gcc-8.2.0-Python-3.7.2
−
|selscan currently implements EHH, iHS, XP-EHH, and nSL, and requires phased data. It should be run separately for each chromosome and population (or population pair for XP-EHH).
+
|SequelTools is a fast and easy to install command-line program that provides a collection of tools for working with multiple SMRTcells of BAM format PacBio Sequel raw sequece data.  
 
|-
 
|-
−
|[https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#home SHAPEIT]
+
|[https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html shapeit]
−
|v2r837
+
|2.20
 
|SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
 
|SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
 
|-
 
|-
−
|[https://bitbucket.org/biobakery/shortbred/wiki/Home shortbred]
+
|[https://www.gnu.org/software/sharutils/ sharutils]
−
|0.9.4
+
|4.15.2-IGB-gcc-4.9.4
−
|ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ('markers'), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.
+
|GNU shar makes so-called shell archives out of many files, preparing them for transmission by electronic mail services, while unshar helps unpacking shell archives after reception.
 
|-
 
|-
−
|[https://github.com/sharpton/shotmap shotmap]
+
|[https://github.com/chanzuckerberg/shasta shasta]
−
|11-4-2014
+
|0.2.0
−
|Shotmap is a software workflow that functionally annotates and compares shotgun metagenomes
+
|The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.
 
|-
 
|-
−
|[http://home.gwu.edu/~wpeng/Software.htm SICER]
+
|[https://github.com/biobakery/shortbred shortbred]
−
|1.1
+
|0.9.5-IGB-gcc-4.9.4-Python-2.7.13
−
|A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
+
|ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.
 
|-
 
|-
−
|[http://www.cbs.dtu.dk/services/SignalP/ signalp]
+
|[https://github.com/bioinf/Sibelia Sibelia]
 +
|3.0.7-IGB-gcc-4.9.4
 +
|Sibelia is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species.
 +
|-
 +
|[https://github.com/najoshi/sickle/ sickle]
 +
|1.33-IGB-gcc-8.2.0
 +
|A windowed adaptive trimming tool for FASTQ files using quality
 +
|-
 +
|[http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp SignalP]
 
|4.1
 
|4.1
−
|SignalP 4.1 server predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive prokaryotes, Gram-negative prokaryotes, and eukaryotes. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks.
+
|Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
 
|-
 
|-
−
|[http://lbbe.univ-lyon1.fr/-SiLiX-.html?lang=fr silix]
+
|[https://github.com/sgoldenlab/simba simba]
−
|1.2.9
+
|1.3.0
−
|The software package SiLiX implements a new algorithm for the clustering of homologous sequences, based on single transitive links (single linkage) with alignment coverage constraints.
+
|The SimBA region of interest (ROI) interface allows users to define and draw ROIs on videos. ROI data can be used to calculate basic descriptive statistics based on animals movements and locations such as:
 
|-
 
|-
−
|[http://www.riverbankcomputing.com/software/sip/intro sip]
+
|singularity
−
|4.16.3
+
|3.4.1<br>3.8.1
−
|SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. It was originally developed to create PyQt, the Python bindings for the Qt toolkit, but can be used to create bindings for any C or C++ library.
+
|Application and environment virtualization
 
|-
 
|-
−
|[http://www.broadinstitute.org/genome_bio/siphy/ siphy]
+
|[https://skylign.org/ skylign]
−
|0.5
+
|1.1-IGB-gcc-4.9.4-Perl-5.24.1
−
|SiPhy implements rigorous statistical tests to detect bases under selection from a multiple alignment data
+
|Skylign is a tool for creating logos representing both sequence alignments and profile hidden Markov models. Submit to the form on the right in order to produce (i) interactive logos for inclusion in webpages, or (ii) static logos for use in documents.
 
|-
 
|-
−
|[http://www.pacb.com/devnet/ smrtanalysis]
+
|[https://sleap.ai/ sleap]
−
|1.4.0, 2.0.1, 2.3.0
+
|1.2.4-IGB-gcc-8.2.0-Python-3.7.2
−
|The SMRT Analysis software suite performs assembly and variant detection analysis of sequencing data generated by the Pacific Biosciences instrument.
+
|SLEAP is an open source deep-learning based framework for multi-animal pose tracking. It can be used to track any type or number of animals and includes an advanced labeling/training GUI for active learning and proofreading.
 
|-
 
|-
−
|[http://snap.cs.berkeley.edu/ snap]
+
|[https://github.com/songjiajia2018/SMART-Aptamer-v1 SMART-Aptamer-v1]
−
|1.0beta.18, 1.0dev.96
+
|20200313-IGB-gcc-4.9.4
−
|SNAP is a new sequence aligner that is 3-20x faster and just as accurate as existing tools like BWA-mem, Bowtie2 and Novoalign. It runs on commodity x86 processors, and supports a rich error model that lets it cheaply match reads with more differences from the reference than other tools.
+
|
 +
|-
 +
|[https://github.com/songjiajia2018/SMART-Aptamer_v2.0 SMART-Aptamer-v2]
 +
|20200315-IGB-gcc-4.9.4
 +
|
 +
|-
 +
|[https://github.com/ruanjue/smartdenovo SMARTdenovo]
 +
|20170916-IGB-gcc-4.9.4-Perl-5.24.1
 +
|SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.
 +
|-
 +
|[https://www.pacb.com/support/software-downloads/ smrtlink]
 +
|10.0.0.108728<br>11.0.0.146107<br>11.1.0.166339<br>8.0.0.80529<br>9.0.0.92188
 +
|PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface.
 +
|-
 +
|[https://github.com/KamilSJaron/smudgeplot smudgeplot]
 +
|0.2.5-IGB-gcc-8.2.0-Python-3.7.2
 +
|This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them.
 +
|-
 +
|[https://snakemake.readthedocs.io/en/stable/ snakemake]
 +
|6.0.5-IGB-gcc-8.2.0-Python-3.7.2
 +
|The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language.  
 
|-
 
|-
 
|[http://korflab.ucdavis.edu/software.html SNAP]
 
|[http://korflab.ucdavis.edu/software.html SNAP]
−
|20131129
+
|2013-11-29-IGB-gcc-4.9.4
 
|(Semi-HMM-based Nucleic Acid Parser) gene prediction tool
 
|(Semi-HMM-based Nucleic Acid Parser) gene prediction tool
 
|-
 
|-
−
|[http://snpeff.sourceforge.net/ SnpEff]
+
|[https://github.com/Edinburgh-Genome-Foundry/SnapGeneReader snapgene-reader]
−
|3.2, 3.3e, 4.2
+
|0.1.19-IGB-gcc-8.2.0-Python-3.7.2
−
|Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
+
|SnapGene Reader is a Python library to parse Snapgene *.dna files into dictionaries or Biopython SeqRecords
 
|-
 
|-
−
|[http://chibba.pgml.uga.edu/snphylo/ snphylo]
+
|[https://github.com/fritzsedlazeck/Sniffles Sniffles]
−
|20160204
+
|1.0.12b-IGB-gcc-8.2.0
−
|Phylogenetic tree is a good tool to infer evolutionary relationships among various organisms so the tree has been used in many evolutionary studies. Consequently, phylogenetic tree based on SNP data have been determined in resequencing projects. However, there was no simple way to determine phylogenetic tree with the huge number of variants determined from resequencing data. Thus, we had developed new pipeline, SNPhylo, to construct phylogenetic tree based on SNP data. With this pipeline, user can construct a phylogenetic tree from a file containing huge SNP data.
+
|Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.  
 
|-
 
|-
−
|[http://soap.genomics.org.cn/soapaligner.html SOAP2]
+
|[http://lowelab.ucsc.edu/snoscan/ snoscan]
−
|2.2
+
|0.9.1-IGB-gcc-4.9.4-Perl-5.24.1<br>0.9.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
−
|SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. The new program features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer. Compared to soap v1, it is one order of magnitude faster.
+
|Search for C/D box methylation guide snoRNA genes in a genomic sequence
 +
|-
 +
|[http://sourceforge.net/projects/snpeff/ snpEff]
 +
|4.3o-Java-1.8.0_121<br>4.3t-Java-1.8.0_152<br>5.0e-Java-15.0.1<br>5.1f-Java-15.0.1
 +
|SnpEff is a variant annotation and effect prediction tool.  It annotates and predicts the effects of genetic variants (such as amino acid changes).
 +
|-
 +
|[https://github.com/magnusmanske/snpomatic snpomatic]
 +
|1.0-IGB-gcc-4.9.4
 +
|SNP-o-matic is a fast, stringent short-read mapping software. It supports a multitude of output types and formats, for uses in filtering reads, alignments, sequence-based genotyping calls, assisted reassembly of contigs etc.
 +
|-
 +
|[https://felixkrueger.github.io/SNPsplit/ SNPsplit]
 +
|0.6.0-IGB-gcc-8.2.0-Perl-5.28.1
 +
|SNPsplit is an allele-specific alignment sorter which is designed to read alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions.
 +
|-
 +
|[http://snver.sourceforge.net/ SNVer]
 +
|0.5.3-Java-1.8.0_121<br>0.5.3-Java-1.8.0_152
 +
|SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained.  
 
|-
 
|-
 
|[http://soap.genomics.org.cn/SOAPdenovo-Trans.html SOAPdenovo-Trans]
 
|[http://soap.genomics.org.cn/SOAPdenovo-Trans.html SOAPdenovo-Trans]
−
|1.02, 1.03
+
|1.03
−
|SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.
+
|SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.  
 
|-
 
|-
−
|[http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo]
+
|[https://github.com/aquaskyline/SOAPdenovo2 SOAPdenovo2]
−
|2.04
+
|r242-IGB-gcc-8.2.0
−
|SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. Now the new version is available. SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.
+
|SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
 
|-
 
|-
−
|[http://soap.genomics.org.cn/soapdenovo.html SOAPdenovo2]
+
|[https://github.com/biocore/songbird songbird]
−
|r240
+
|1.0.3-IGB-gcc-4.9.4-Python-3.6.1
−
|SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. Now the new version is available. SOAPdenovo2, which has the advantage of a new algorithm design that reduces memory consumption in graph construction, resolves more repeat regions in contig assembly, increases coverage and length in scaffold construction, improves gap closing, and optimizes for large genome.
+
|Establishing microbial composition measurement standards with reference frames
 
|-
 
|-
−
|[http://soap.genomics.org.cn/about.html SOAPec]
+
|[https://bioinfo.lifl.fr/RNA/sortmerna/ sortmerna]
−
|2.01, 2.02
+
|2.1<br>4.3.6
−
|The read correction package is a short-read correction tool and part of SOAPdenovo . It is specially designed to correct Illum ina GA short reads.
+
|SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences.  
 
|-
 
|-
−
|[http://soap.genomics.org.cn/soapdenovo.html SOAPErrorCorrection]
+
|[https://github.com/biota/sourcetracker2 sourcetracker]
−
|0.04
+
|2.0.1-IGB-gcc-4.9.4-Python-3.6.1
−
|Another correction tool for SOAPdenovo
+
|Bayesian community-wide culture-independent microbial source tracking
 
|-
 
|-
−
|[http://soap.genomics.org.cn/about.html SOAPGapCloser]
+
|[https://github.com/sourmash-bio/sourmash sourmash]
−
|1.12
+
|4.6.1-IGB-gcc-8.2.0-Python-3.10.1
−
|The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads.
+
|Quickly search, compare, and analyze genomic and metagenomic data sets.
 
|-
 
|-
−
|[http://soap.genomics.org.cn/about.html SOAPprepare]
+
|[http://http://sox.sourceforge.net/ SoX]
−
|0.1
+
|14.4.2-IGB-gcc-4.9.4
−
|Data Preparation Module generates necessary data for SOAPdenovo to run 'map' and 'scaff' steps from Contigs generated by SOAPdenovo or other assemblers with various length of kmer.
+
|Sound eXchange, the Swiss Army knife of audio manipulation
 
|-
 
|-
−
|[http://solexaqa.sourceforge.net/ SolexaQA]
+
|[https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger spaceranger]
−
|3.1.2
+
|1.0.0<br>1.1.0<br>1.2.2<br>1.3.0<br>2.0.0<br>2.1.0
−
|SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data.
+
|Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield and fluorescence microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.
 
|-
 
|-
−
|[https://github.com/orionzhou/SPADA/ SPADA]
+
|[https://spacy.io/ spaCy]
−
|20150512
+
|2.3.2-IGB-gcc-4.9.4-Python-3.6.1
−
|SPADA is a computational pipeline that, provided a multiple sequence alignment for an interested gene/protein family, identifies all members of this family in a target genome sequence. This pipeline comes with manually-curated protein sequence alignments for all Cysteine-Rich Peptides family in plant genomes.
+
|spaCy is designed to help you do real work — to build real products, or gather real insights. The library respects your time, and tries to avoid wasting it. It's easy to install, and its API is simple and productive.
 
|-
 
|-
−
|[http://bioinf.spbau.ru/spades spades]
+
|[http://cab.spbu.ru/software/spades/ SPAdes]
−
|3.0.0, 3.1.1, 3.5.0, 3.6.2, 3.7.1, 3.10.0, 3.10.1
+
|3.10.1-IGB-gcc-4.9.4-Python-2.7.13<br>3.11.0-IGB-gcc-4.9.4-Python-2.7.13<br>3.11.0-IGB-gcc-4.9.4-Python-3.6.1<br>3.11.1-IGB-gcc-4.9.4-Python-3.6.1<br>3.13.1-IGB-gcc-8.2.0-Python-3.7.2<br>3.14.1-IGB-gcc-8.2.0-Python-3.7.2<br>3.15.0-IGB-gcc-8.2.0-Python-3.7.2<br>3.15.3-IGB-gcc-8.2.0-Python-3.7.2<br>3.15.5-IGB-gcc-8.2.0-Python-3.7.2
 
|SPAdes . St. Petersburg genome assembler . is intended for both standard isolates and single-cell MDA bacteria assemblies.
 
|SPAdes . St. Petersburg genome assembler . is intended for both standard isolates and single-cell MDA bacteria assemblies.
 
|-
 
|-
−
|[http://sourceforge.net/p/speciateit/code/HEAD/tree/ speciateit]
+
|[https://github.com/sparsehash/sparsehash sparsehash]
−
|184
+
|2.0.3-IGB-gcc-4.9.4<br>2.0.3-IGB-gcc-8.2.0
−
|This is a beta version of a speciation pipeline for 16S rRNA amplicon data. In principle, the pipeline can be used for speciation based on any highly preserved gene.
+
|This directory contains several hash-map implementations, similar inAPI to SGIs hash_map class, but with different performance characteristics.
 
|-
 
|-
−
|[http://sourceforge.net/p/speciateit/code/HEAD/tree/ speciate_it]
+
|[http://vfsmspineagent.fsm.northwestern.edu/ Spine]
−
|184
+
|0.2.1-IGB-gcc-4.9.4
−
|This is a beta version of a speciation pipeline for 16S rRNA amplicon data. In principle, the pipeline can be used for speciation based on any highly preserved gene.
 
−
|-
 
−
|[http://vfsmspineagent.fsm.northwestern.edu/cgi-bin/age_finder.cgi spine]
 
−
|0.1.2
 
 
|Spine identifies a core genome from input genomic sequences. Sequences are aligned using Nucmer and regions found to be in common between all or a user-defined subset of genomes will be returned.
 
|Spine identifies a core genome from input genomic sequences. Sequences are aligned using Nucmer and regions found to be in common between all or a user-defined subset of genomes will be returned.
 
|-
 
|-
−
|[https://github.com/GuyAllard/SPINGO SPINGO]
+
|[http://www.sqlite.org/ SQLite]
−
|1.1
+
|3.17.0-IGB-gcc-4.9.4<br>3.17.0-IGB-gcc-8.2.0<br>3.30.1-IGB-gcc-4.9.4
−
|SPecies level IdentificatioN of metaGenOmic amplicons (alternatively: an olde English word meaning ‘strong beer’)
+
|SQLite: SQL Database Engine in a C Library
 
|-
 
|-
−
|[http://www.ncbi.nlm.nih.gov/Traces/sra/?view=software sratoolkit]
+
|[http://eddylab.org/software.html squid]
−
|2.1.16, 2.3.5-2, 2.5.1, 2.5.7, 2.8.1
+
|1.9g-IGB-gcc-4.9.4
−
|The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format (Note that this is not required for submission).
+
|A C library that is bundled with much of the above software. C function library for sequence analysis.
 
|-
 
|-
−
|[http://srna-tools.cmp.uea.ac.uk/ srna-tools]
+
|[http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std SRA-Toolkit]
−
|20130118
+
|2.10.5<br>2.10.9<br>2.8.2-1<br>3.0.0
−
|A variety of tools for the analysis of high-throughput small RNA data.
+
|The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format
 
|-
 
|-
−
|[https://www.sanger.ac.uk/resources/software/ssaha/ ssaha2]
+
|[http://www.sanger.ac.uk/science/tools/ssaha2-0 ssaha2]
−
|2.5.5
+
|2.5.5-IGB-gcc-4.9.4
−
|SSAHA is a software tool for very fast matching and alignment of DNA sequences.  It achieves its fast search speed by converting sequence information into a 'hash table' data structure, which can then be searched very rapidly for matches.
+
|SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.
 
|-
 
|-
−
|[http://www.baseclear.com SSPACE-premium]
+
|[http://www.sanger.ac.uk/science/tools/ssaha2-0 ssaha_pileup]
−
|2.3.1
+
|0.6-IGB-gcc-4.9.4
−
|SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired end libraries, or even a combination.
+
|SSAHA2: Sequence Search and Alignment by Hashing Algorithm
 
|-
 
|-
−
|[http://www.baseclear.com SSPACE]
+
|SSW
−
|1.1
+
|
−
|SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired end libraries, or even a combination.
+
|SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.
 
|-
 
|-
−
|[http://creskolab.uoregon.edu/stacks/ stacks]
+
|[http://creskolab.uoregon.edu/stacks/ Stacks]
−
|0.9996, 0.99994, 1.2.0, 1.40, 1.44
+
|1.47-IGB-gcc-4.9.4<br>2.54-IGB-gcc-8.2.0<br>2.62-IGB-gcc-8.2.0
 
|Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
 
|Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
 
|-
 
|-
−
|[http://compbio.mit.edu/starmp/ STAR-MP]
+
|[https://github.com/alexdobin/STAR STAR]
−
|1.0
+
|2.5.3a-IGB-gcc-4.9.4<br>2.6.0c-IGB-gcc-4.9.4<br>2.6.1b-IGB-gcc-4.9.4<br>2.7.0d-IGB-gcc-8.2.0<br>2.7.0f-IGB-gcc-8.2.0<br>2.7.10a-IGB-gcc-8.2.0<br>2.7.3a-IGB-gcc-8.2.0<br>2.7.4a-IGB-gcc-8.2.0<br>2.7.6a-IGB-gcc-8.2.0
−
|Species Tree informed Architecture Reconstruction - Maximum Parsimony
+
|STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
 +
|-
 +
|[https://github.com/STAR-Fusion/STAR-Fusion/wiki STAR-Fusion]
 +
|1.6.0-IGB-gcc-4.9.4
 +
|STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads.
 
|-
 
|-
−
|[https://github.com/alexdobin/STAR STAR]
+
|[http://www.crypticlineage.net/pages/software.html strauto]
−
|2.4.0h1, 2.4.2a, 2.5.0a, 2.5.1b
+
|1-IGB-gcc-4.9.4
−
|STAR: Spliced Transcripts Alignment to a Reference
+
|Automation and Parallelization of STRUCTURE Analysis
 
|-
 
|-
−
|[http://www.stat.osu.edu/~lkubatko/software/STEM/ STEM-hy]
+
|[https://github.com/Illumina/strelka strelka]
−
|1.0
+
|2.9.9
−
|STEM-hy is a program for inferring maximum likelihood species trees from a collection of estimated gene trees under the coalescent model.
+
|Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.  
 
|-
 
|-
−
|[http://ccb.jhu.edu/software/stringtie/ stringtie]
+
|[http://ccb.jhu.edu/software/stringtie/ StringTie]
−
|1.2.4, 1.3.3
+
|1.3.3-IGB-gcc-4.9.4<br>1.3.6-IGB-gcc-4.9.4
−
|StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It uses a novel network flow algorithm as well as an optional de novo assembly step to assemble and quantitate full-length transcripts representing multiple splice variants for each gene locus. Its input can include not only the alignments of raw reads used by other transcript assemblers, but also alignments longer sequences that have been assembled from those reads.In order to identify differentially expressed genes between experiments, StringTie's output can be processed by specialized software like Ballgown, Cuffdiff or other programs (DESeq2, edgeR, etc.).
+
|StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
 
|-
 
|-
−
|[http://pritchardlab.stanford.edu/structure.html structure]
+
|[https://github.com/gpertea/stringtie stringtie]
−
|2.3.4
+
|2.1.1-IGB-gcc-4.9.4
−
|The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.
+
|Transcript assembly and quantification for RNA-Seq
 
|-
 
|-
−
|[http://veda.cs.uiuc.edu/wholegenome/stubb.tar.gz stubb]
+
|[https://web.stanford.edu/group/pritchardlab/structure.html structure]
−
|2.1
+
|2.3.4-IGB-gcc-4.9.4
−
|
+
|The program structure is a free software package for using multi-locus genotype data to investigate population structure.
 
|-
 
|-
−
|[http://subread.sourceforge.net/ subread]
+
|[http://subread.sourceforge.net/ Subread]
−
|1.3.6, 1.4.5-p1, 1.4.6-p1, 1.4.6-p4, 1.5.0
+
|1.5.2-IGB-gcc-4.9.4<br>1.6.3-IGB-gcc-4.9.4<br>2.0.0-IGB-gcc-8.2.0<br>2.0.4-IGB-gcc-8.2.0
−
|The Subread package comprises a suite of software programs for processing next-gen sequencing read data including:
+
|High performance read alignment, quantification and mutation discovery
 
|-
 
|-
−
|[https://pypi.python.org/pypi/Sunflower Sunflower]
+
|[http://faculty.cse.tamu.edu/davis/suitesparse.html SuiteSparse]
−
|1.1.0
+
|5.4.0-IGB-gcc-4.9.4-METIS-5.1.0<br>5.8.1-IGB-gcc-8.2.0
−
|Sunflower models the simultaneous binding of transcription factors to DNA. It uses a hidden Markov model that resembles a sunflower.
+
|SuiteSparse is a collection of libraries manipulate sparse matrices.
 
|-
 
|-
−
|[http://software.10xgenomics.com/de-novo-assembly/overview/welcome supernova]
+
|[http://computation.llnl.gov/projects/sundials SUNDIALS]
−
|1.0.0, 1.1.0, 1.1.2, 1.1.5, 1.2.0
+
|2.6.2-IGB-gcc-4.9.4
−
|Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a whole-genome library of an individual DNA source.
+
|SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
 
|-
 
|-
−
|[http://supfam.org/SUPERFAMILY/ supfam]
+
|[https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Supernova]
−
|1.75
+
|1.1.5<br>1.2.0<br>1.2.1<br>2.0.0<br>2.0.1<br>2.1.0<br>2.1.1
−
|SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
+
|Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source. A key feature of Supernova is that it creates diploid assemblies, thus separately representing maternal and paternal chromosomes over very long distances.
 
|-
 
|-
−
|[http://svdetect.sourceforge.net/Site/Home.html SVDetect]
+
|[https://github.com/fritzsedlazeck/SURVIVOR SURVIVOR]
−
|r0.7m
+
|1.0.7-IGB-gcc-8.2.0
−
|SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies
+
|SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.
 
|-
 
|-
 
|[https://github.com/hall-lab/svtools svtools]
 
|[https://github.com/hall-lab/svtools svtools]
−
|0.2.0
+
|0.5.1-IGB-gcc-4.9.4-Python-2.7.13
−
|svtools is a suite of utilities designed to help bioinformaticians construct and explore cohort-level structural variation calls. It is designed to efficiently merge and genotype calls from speedseq sv across thousands to tens of thousands of genomes
+
|Comprehensive utilities to explore structural variations in genomes
 
|-
 
|-
 
|[https://github.com/hall-lab/svtyper svtyper]
 
|[https://github.com/hall-lab/svtyper svtyper]
−
|0.0.4
+
|0.7.1-IGB-gcc-4.9.4-Python-2.7.13
−
|Bayesian genotyper for structural variants
+
|SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data.
 +
|-
 +
|[http://swift-lang.org/Swift-T/ swift-t]
 +
|1.3-IGB-gcc-4.9.4
 +
|Swift/T is a completely new implementation of the Swift language for high-performance computing. In this implementation, the Swift script is translated into an MPI program that uses the Turbine (hence, /T) and ADLB runtime libraries for highly scalable dataflow processing over MPI, without single-node bottlenecks.
 +
|-
 +
|[http://www.swig.org/ SWIG]
 +
|2.0.12-IGB-gcc-4.9.4-Python-2.7.13<br>3.0.12-IGB-gcc-4.9.4-Python-2.7.13<br>3.0.12-IGB-gcc-4.9.4-Python-2.7.13-Perl-5.24.1
 +
|SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. - Homepage: http://www.swig.org/
 +
|-
 +
|[https://www.synapse.org/ synapseclient]
 +
|1.9.2-IGB-gcc-4.9.4-Python-3.6.1
 +
|Synapse is an open source software platform that data scientists can use to carry out, track, and communicate their research in real time.
 +
|-
 +
|Szip
 +
|
 +
|Szip compression software, providing lossless compression of scientific data
 +
|-
 +
|[https://t3f.readthedocs.io/en/latest/index.html t3f]
 +
|1.1.0-IGB-gcc-4.9.4-Python-3.6.1<br>1.1.0-IGB-gcc-4.9.4-Python-3.6.1-TF-2.0.3<br>20200316-IGB-gcc-4.9.4-Python-3.6.1-TF-2.0.3<br>20200316-IGB-gcc-4.9.4-Python-3.6.1-TF-2.2.0
 +
|t3f is a library for working with Tensor Train decomposition.
 +
|-
 +
|[http://samtools.sourceforge.net tabix]
 +
|0.2.6-IGB-gcc-4.9.4
 +
|Generic indexer for TAB-delimited genome position files
 
|-
 
|-
−
|[http://swig.org/ swig]
+
|[https://github.com/ekg/tabixpp tabixpp]
−
|3.0.8
+
|1.1.0-IGB-gcc-8.2.0
−
|SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. SWIG is used with different types of target languages including common scripting languages such as Javascript, Perl, PHP, Python, Tcl and Ruby.
+
|This is a C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.
 
|-
 
|-
−
|[http://samtools.sourceforge.net/tabix.shtml tabix]
+
|[https://github.com/lvclark/tagdigger tagdigger]
−
|0.2.6
+
|1.1-IGB-gcc-4.9.4-Python-3.6.1
−
|Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line.
+
|TagDigger is a program for processing FASTQ files from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) experiments.  
 
|-
 
|-
−
|[https://github.com/firecat53/tabview tabview]
+
|[https://github.com/hyeshik/tailseeker tailseeker]
−
|1.4.2
+
|3.2.1
−
|View a CSV file in a spreadsheet-like display.
+
|Tailseeker is the official pipeline for TAIL-seq, which measures poly(A) tail lengths and 3′-end modifications with Illumina SBS sequencers.
 
|-
 
|-
−
|[http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?targetp targetp]
+
|[https://github.com/songlab-cal/tape TAPE]
−
|1.1
+
|0.4-IGB-gcc-4.9.4-Python-3.6.1<br>20191209-IGB-gcc-4.9.4-Python-3.6.1
−
|Secretory signal peptides, mitochondrial targeting peptides and chloroplast transit peptides in eukaryotes.
+
|Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
 
|-
 
|-
−
|[http://sourceforge.net/projects/tasr-pipeline/ tasr]
+
|[http://www.gnu.org/software/tar/tar.html tar]
−
|1.0
+
|1.32-IGB-gcc-8.2.0
−
|TASR is a bioinformatic pipeline that can annotate Transposable elements using siRNAs mapping
+
|tar: The GNU tape archiver
 
|-
 
|-
−
|[http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&Itemid=119 tassel]
+
|[http://www.maizegenetics.net/tassel TASSEL]
−
|3.0, 4.0, 5.0
+
|5.2.28-Java-1.8.0_121<br>5.2.28-Java-1.8.0_152
−
|While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes
+
|While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes  
 
|-
 
|-
−
|[https://www.threadingbuildingblocks.org/ tbb]
+
|tbb
−
|4.2-3, 4.3, 4.4
+
|
−
|Intel Threading Building Blocks (Intel TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.
+
|Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.
 
|-
 
|-
 
|[https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ tbl2asn]
 
|[https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ tbl2asn]
−
|20170612
+
|20180516<br>20190117<br>20200203<br>20200707
−
|Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank. It uses many of the same functions as Sequin but is driven generally by data files. Tbl2asn generates .sqn files for submission to GenBank. Additional manual editing is not required before submission.
+
|Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank
 +
|-
 +
|Tcl
 +
|
 +
|Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language,suitable for a very wide range of uses, including web and desktop applications, networking, administration,testing and many more.
 +
|-
 +
|[https://github.com/lanpa/tensorboardX tensorboardX]
 +
|1.9-IGB-gcc-4.9.4-Python-3.6.1<br>2.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.1-IGB-gcc-8.2.0-Python-3.7.2<br>2.5.1-IGB-gcc-8.2.0
 +
|Tensorboard for PyTorch.
 +
|-
 +
|[https://www.tensorflow.org/ Tensorflow]
 +
|1.15.2-IGB-gcc-4.9.4-Python-3.6.1<br>1.2.1-IGB-gcc-4.9.4-Python-2.7.13<br>2.2.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.8.2-IGB-gcc-8.2.0-Python-3.7.2<br>2.9.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|An open-source software library for Machine Intelligence
 
|-
 
|-
−
|[http://www.tcoffee.org/ tcoffee]
+
|[https://www.tensorflow.org/ Tensorflow-GPU]
−
|10-r1613
+
|1.13.1-IGB-gcc-4.9.4-Python-3.6.1<br>1.14.0-IGB-gcc-4.9.4-Python-3.6.1<br>1.2.1-IGB-gcc-4.9.4-Python-3.6.1<br>1.5.1-IGB-gcc-4.9.4-Python-3.6.1<br>1.9.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.0.3-IGB-gcc-4.9.4-Python-3.6.1<br>2.11.0-IGB-gcc-8.2.0-Python-3.7.2<br>2.2.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.3.1-IGB-gcc-8.2.0-Python-3.7.2<br>2.5.3-IGB-gcc-8.2.0-Python-3.7.2<br>2.6.5-IGB-gcc-8.2.0-Python-3.7.2<br>2.9.1-IGB-gcc-8.2.0-Python-3.7.2
−
|A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
+
|An open-source software library for Machine Intelligence
 
|-
 
|-
−
|[https://www.gnu.org/software/texinfo/ texinfo]
+
|[https://github.com/tensorflow/models TensorFlowModels]
−
|6.1
+
|1.11-IGB-gcc-4.9.4-Python-3.6.1<br>20171113-IGB-gcc-4.9.4-Python-3.6.1
−
|Texinfo is the official documentation format of the GNU project. It was invented by Richard Stallman and Bob Chassell many years ago, loosely based on Brian Reid's Scribe and other formatting languages of the time. It is used by many non-GNU projects as well.
+
|This repository contains a number of different models implemented in TensorFlow:
 
|-
 
|-
−
|[https://www.tug.org/texlive/ texlive]
+
|[http://tensorly.org/stable/home.html tensorly]
−
|2015
+
|0.4.2-IGB-gcc-4.9.4-Python-3.6.1
−
|TeX Live is an easy way to get up and running with the TeX document production system. It provides a comprehensive TeX system with binaries for most flavors of Unix, including GNU/Linux, and also Windows. It includes all the major TeX-related programs, macro packages, and fonts that are free software, including support for many languages around the world.
+
|Simple and Fast Tensor Learning in Python
 
|-
 
|-
−
|[http://deeplearning.net/software/theano/ Theano]
+
|[https://github.com/mhammell-laboratory/TEtranscripts TEtranscripts]
−
|0.7.0
+
|2.2.1-IGB-gcc-8.2.0-Python-3.7.2
−
|Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
+
|TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements. TEtranscripts then performs differential analysis using DESeq2.
 
|-
 
|-
−
|[http://www.regulatory-genomics.org/thor-2 THOR]
+
|Tk
−
|0.1
+
|
−
|THOR is an HMM-based approach to detect and analyze differential peaks in two sets of ChIP-seq data from distinct biological conditions with replicates. THOR performs genomic signal processing, peak calling and p-value calculation in an integrated framework.
+
|Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
 
|-
 
|-
−
|[http://www.cbs.dtu.dk/services/TMHMM-2.0/ tmhmm]
+
|[https://services.healthtech.dtu.dk/service.php?TMHMM-2.0 TMHMM]
−
|2.0
+
|2.0c
 
|Prediction of transmembrane helices in proteins
 
|Prediction of transmembrane helices in proteins
 
|-
 
|-
−
|[http://tophat.cbcb.umd.edu/ tophat]
+
|[https://github.com/DataBiosphere/toil toil]
−
|1.4.1
+
|5.3.0-IGB-gcc-8.2.0-Python-3.7.2
−
|TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
+
|Toil is a scalable, efficient, cross-platform (Linux & macOS) pipeline management system, written entirely in Python, and designed around the principles of functional programming.
 
|-
 
|-
−
|[http://tophat.cbcb.umd.edu/ tophat2]
+
|[https://github.com/tolkit/tolkein tolkein]
−
|2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10, 2.0.13, 2.1.1
+
|0.2.6-IGB-gcc-4.9.4-Python-3.6.1
−
|TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
+
|Tree of Life Kit of Evolutionary Informatics Novelties
 
|-
 
|-
−
|[https://github.com/TransDecoder/TransDecoder transdecoder]
+
|[https://github.com/nanoporetech/tombo/ tombo]
−
|2.0.1
+
|1.5-IGB-gcc-4.9.4-Python-3.6.1
 +
|Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. Tombo also provides tools for the analysis and visualization of raw nanopore signal.
 +
|-
 +
|[http://ccb.jhu.edu/software/tophat/index.shtml TopHat]
 +
|1.4.1<br>2.1.1-IGB-gcc-4.9.4
 +
|TopHat is a fast splice junction mapper for RNA-Seq reads.
 +
|-
 +
|[https://github.com/torch/distro Torch]
 +
|20171018-IGB-gcc-4.9.4-Python-3.6.1
 +
|Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation.
 +
|-
 +
|[https://github.com/ncullen93/torchsample torchsample]
 +
|0.1.3-IGB-gcc-4.9.4-Python-3.6.1
 +
|High-Level Training, Data Augmentation, and Utilities for Pytorch
 +
|-
 +
|[https://github.com/TransDecoder/TransDecoder/wiki TransDecoder]
 +
|5.1.0-IGB-gcc-4.9.4-Perl-5.24.1<br>5.5.0-IGB-gcc-4.9.4-Perl-5.24.1<br>5.7.0-IGB-gcc-8.2.0-Perl-5.28.1
 
|TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
 
|TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
 
|-
 
|-
 
|[http://hibberdlab.com/transrate/ transrate]
 
|[http://hibberdlab.com/transrate/ transrate]
−
|1.0.1, 1.0.3
+
|1.0.3
−
|Transrate analyses a transcriptome assembly in three key ways:
+
|Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies.
 
|-
 
|-
−
|[http://code.google.com/p/treemix/ treemix]
+
|[https://github.com/laurikari/tre tre]
−
|1.12
+
|20161208-IGB-gcc-4.9.4
 +
|TRE is a lightweight, robust, and efficient POSIX compliant regexp matching library with some exciting features such as approximate (fuzzy) matching.The matching algorithm used in TRE uses linear worst-case time in the length of the text being searched, and quadratic worst-case time in the length of the used regular expression.In other words, the time complexity of the algorithm is O(M^2N), where M is the length of the regular expression and N is the length of the text. The used space is also quadratic on the length of the regex, but does not depend on the searched string. This quadratic behaviour occurs only on pathological cases which are probably very rare in practice.
 +
|-
 +
|[https://bitbucket.org/nygcresearch/treemix treemix]
 +
|1.13-IGB-gcc-4.9.4
 
|TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.
 
|TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.
 
|-
 
|-
 
|[http://tandem.bu.edu/trf/trf.html trf]
 
|[http://tandem.bu.edu/trf/trf.html trf]
−
|4.04
+
|4.0.9
−
|Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
+
|Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
 +
|-
 +
|[http://www.usadellab.org/cms/?page=trimmomatic Trimmomatic]
 +
|0.33-Java-1.8.0_152<br>0.36-Java-1.8.0_152<br>0.38-Java-1.8.0_152<br>0.39-Java-1.8.0_201
 +
|Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
 +
|-
 +
|[http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Trim_Galore]
 +
|0.4.4-IGB-gcc-4.9.4<br>0.6.5-IGB-gcc-4.9.4
 +
|A wrapper tool around Cutadapt and FastQC to consistently apply  quality and adapter trimming to FastQ files, with some extra functionality for  MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
 +
|-
 +
|[http://trinityrnaseq.github.io/ Trinity]
 +
|2.10.0-IGB-gcc-8.2.0<br>2.14.0-IGB-gcc-8.2.0<br>2.15.1-IGB-gcc-8.2.0<br>2.4.0-IGB-gcc-4.9.4<br>2.5.0-IGB-gcc-4.9.4<br>2.6.5-IGB-gcc-4.9.4<br>2.8.5-IGB-gcc-4.9.4
 +
|Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
 +
|-
 +
|[https://trinotate.github.io/ Trinotate]
 +
|3.1.1-IGB-gcc-4.9.4-Perl-5.24.1<br>3.2.1-IGB-gcc-4.9.4-Perl-5.24.1<br>4.0.0-IGB-gcc-8.2.0-Perl-5.28.1
 +
|Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
 +
|-
 +
|[http://lowelab.ucsc.edu/tRNAscan-SE/ tRNAscan-SE]
 +
|1.3.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
 +
|tRNAscan-SE: a tool for finding transfer RNAs
 +
|-
 +
|[https://experts.illinois.edu/en/publications/truesight-self-training-algorithm-for-splice-junction-detection-u truesight]
 +
|0.06-IGB-gcc-4.9.4
 +
|A Self-training Algorithm for Splice Junction Detection using RNA-seq.
 +
|-
 +
|[https://github.com/rrwick/Trycycler Trycycler]
 +
|0.4.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.
 +
|-
 +
|[https://github.com/Gaius-Augustus/TSEBRA TSEBRA]
 +
|1.0.3-IGB-gcc-8.2.0
 +
|TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER11 and BRAKER22 predicitons to increase their accuracies.
 +
|-
 +
|[https://github.com/Generade-nl/TULIP TULIP]
 +
|20170513-IGB-gcc-4.9.4-Perl-5.24.1
 +
|Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these.
 +
|-
 +
|udunits
 +
|
 +
|UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
 +
|-
 +
|[https://biobank.ndph.ox.ac.uk/showcase/download.cgi ukbiobank]
 +
|20190130
 +
|Biobank download software
 +
|-
 +
|umap-learn
 +
|0.4.6-IGB-gcc-4.9.4-Python-3.6.1<br>0.4.6-IGB-gcc-8.2.0-Python-3.7.2<br>0.5.2-IGB-gcc-8.2.0-Python-3.7.2
 +
|Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
 +
|-
 +
|[https://github.com/CGATOxford/UMI-tools umi-tools]
 +
|1.0.1-IGB-gcc-8.2.0-Python-3.7.2
 +
|Tools for handling Unique Molecular Identifiers in NGS data sets
 +
|-
 +
|[https://github.com/PacificBiosciences/unanimity/ unanimity]
 +
|20180307-IGB-gcc-4.9.4
 +
|C++ library and its applications to generate and process accurate consensus sequences
 +
|-
 +
|[https://github.com/rrwick/Unicycler Unicycler]
 +
|0.4.3-IGB-gcc-4.9.4-Python-3.6.1<br>0.4.4-IGB-gcc-4.9.4-Python-3.6.1<br>0.4.8-IGB-gcc-4.9.4-Python-3.6.1
 +
|Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
 
|-
 
|-
−
|[http://www.usadellab.org/cms/?page=trimmomatic trimmomatic]
+
|[https://github.com/churchlab/UniRep unirep]
−
|0.22, 0.27, 0.30, 0.32, 0.33, 0.36
+
|20200303-IGB-gcc-4.9.4-Python-3.6.1
−
|Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.
+
|UniRep, a mLSTM "babbler" deep representation learner for protein engineering informatics.
 
|-
 
|-
−
|[http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ trim_galore]
+
|[https://www.rarlab.com/ unrar]
−
|0.3.7, 0.4.1
+
|5.7.3-IGB-gcc-4.9.4
−
|A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
+
|RAR is a powerful archive manager.
 
|-
 
|-
−
|[http://trinityrnaseq.sourceforge.net/ trinityrnaseq-intel]
+
|[http://www.drive5.com/usearch/index.html USEARCH]
−
|r2013-02-25, r2014-04-13, r2014-07-17
+
|11.0.667<br>11.0.667-akent<br>6.1.544<br>7.0.1090<br>9.2.64
−
|Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
+
|USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
 
|-
 
|-
−
|[http://trinityrnaseq.sourceforge.net/ trinityrnaseq]
+
|[https://www.kernel.org/pub/linux/utils/util-linux util-linux]
−
|2.0.6, 2.1.1, 2.2.0, 2.4.0, r2012-06-08, r2013-02-25, r2013-08-14, r2014-04-13, r2014-07-17
+
|2.34-IGB-gcc-4.9.4
−
|Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
+
|Set of Linux utilities
 
|-
 
|-
−
|[http://trinotate.sourceforge.net/ trinotate]
+
|[http://valgrind.org/downloads/ valgrind]
−
|2.0.2, 3.0.1, r20130826, r20140708
+
|3.13.0-IGB-gcc-4.9.4
−
|Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
+
|Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.
 
|-
 
|-
−
|[http://selab.janelia.org/tRNAscan-SE/ tRNAscan-SE]
+
|[http://www.ub.edu/softevol/variscan/ variscan]
−
|1.23
+
|2.0.3-IGB-gcc-4.9.4
−
|tRNAscan-SE detects ~99% of eukaryotic nuclear or prokaryotic tRNA genes, with a false positive rate of less than one per 15 gigabases, and with a search speed of about 30 kb/second.
+
|VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale. Among other features,
 
|-
 
|-
−
|[http://bioen-compbio.bioen.illinois.edu/TrueSight/ truesight]
+
|VarScan
−
|0.06
+
|2.3.9-Java-1.8.0_152
−
|Self-training Algorithm for Splice Junction Detection using RNA-seq.
+
|
 
|-
 
|-
−
|[http://drive5.com/usearch/manual/uchime_algo.html uchime]
+
|[https://github.com/10XGenomics/vartrix vartrix]
−
|4.2.40
+
|1.1.22
−
|UCHIME is an algorithm for detecting chimeric sequences. It is implemented in the uchime_ref and uchime_denovo commands.
+
|VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data. VarTrix will take a set of previously defined variant calls and use that to identify those variants in the single cell data.
 
|-
 
|-
−
|[http://hgdownload.soe.ucsc.edu/admin/exe ucsc]
+
|[http://www.cse.lehigh.edu/~chen/software.htm VASP-E]
−
|20130806, v312
+
|20190225-IGB-gcc-4.9.4<br>20191112-IGB-gcc-4.9.4
−
|This directory contains Genome Browser and Blat application binaries built for standalone command-line use on various supported Linux and UNIX platforms.
+
|VASP and VASP-E explore the idea that a solid geometric representation of molecular structures can be used to automatically deconstruct proteins into functional elements for the study of binding specificity.
 
|-
 
|-
−
|[http://www.unidata.ucar.edu/software/udunits/ udunits]
+
|[http://csg.sph.umich.edu/liyanmin/vcfCodingSnps/index.shtml vcfCodingSnps]
−
|2.1.24
+
|1.5
−
|The UDUNITS package supports units of physical quantities. Its C library provides for arithmetic manipulation of units and for conversion of numeric values between compatible units. The package contains an extensive unit database, which is in XML format and user-extendable. The package also contains a command-line utility for investigating units and converting values.
+
|vcfCodingSnps is a SNP annotation tool that annotates coding variants in VCF files.  
 
|-
 
|-
−
|[http://www.drive5.com/usearch/ usearch]
+
|[https://github.com/vcflib/vcflib vcflib]
−
|4.2.66, 5.2.32, 5.2.236, 6.0.307, 6.1.544, 7.0.959, 7.0.1090, 8.0.1517
+
|1.0.0-rc2-IGB-gcc-8.2.0<br>1.0.2-IGB-gcc-8.2.0
−
|USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
+
|a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
 
|-
 
|-
−
|[http://useq.sourceforge.net/ USeq]
+
|[https://vcftools.github.io VCFtools]
−
|8.5.1
+
|0.1.15-IGB-gcc-4.9.4-Perl-5.24.1<br>0.1.16-IGB-gcc-8.2.0-Perl-5.28.1
−
|USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.
+
|The aim of VCFtools is to provide  easily accessible methods for working with complex  genetic variation data in the form of VCF files.
 
|-
 
|-
−
|[http://vcftools.sourceforge.net/ vcftools]
+
|[https://github.com/velocyto-team/velocyto.py velocyto]
−
|0.1.7, 0.1.11, 0.1.12b, 0.1.13, 0.1.14
+
|0.17.17-IGB-gcc-4.9.4-Python-3.6.1
−
|VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
+
|Velocyto is a library for the analysis of RNA velocity.
 
|-
 
|-
−
|[http://www.ebi.ac.uk/~zerbino/velvet/ velvet-kmer245]
+
|[https://github.com/velocyto-team/velocyto.R velocyto.R]
−
|1.2.10
+
|20190527-IGB-gcc-4.9.4-R-3.4.2
−
|Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
+
|RNA velocity estimation in R
 
|-
 
|-
 
|[https://www.ebi.ac.uk/~zerbino/velvet/ velvet]
 
|[https://www.ebi.ac.uk/~zerbino/velvet/ velvet]
−
|1.1.04, 1.2.08, 1.2.10
+
|1.2.10-IGB-gcc-4.9.4-kmer_121<br>1.2.10-IGB-gcc-8.2.0-kmer_121
−
|Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
+
|Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
 +
|-
 +
|[https://github.com/Ensembl/ensembl-vep VEP]
 +
|92.4-IGB-gcc-4.9.4-Perl-5.24.1
 +
|VEP (Variant Effect Predictor) predicts the functional effects of genomic variants.
 +
|-
 +
|[https://github.com/vgteam/vg vg]
 +
|1.15.0
 +
|variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
 +
|-
 +
|[https://github.com/IGBIllinois/VICSIN VICSIN]
 +
|0.5-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13<br>0.5.1-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13<br>0.5.2-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13<br>1.0-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13<br>dev
 +
|VICSIN = Viral, Integrative, and Conjugative Sequence Identification and Networking
 +
|-
 +
|[https://www.tbi.univie.ac.at/RNA/ ViennaRNA]
 +
|2.4.14-IGB-gcc-4.9.4<br>2.4.2-IGB-gcc-4.9.4
 +
|The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
 +
|-
 +
|[https://github.com/simroux/VirSorter VirSorter]
 +
|20170215-IGB-gcc-4.9.4-Perl-5.24.1
 +
|VirSorter: mining viral signal from microbial genomic data.
 +
|-
 +
|[https://github.com/jiarong/VirSorter2 VirSorter2]
 +
|2.2.3
 +
|irSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.
 +
|-
 +
|[https://bitbucket.org/genomicepidemiology/virulencefinder/ virulencefinder]
 +
|2.0.4-IGB-gcc-8.2.0-Python-3.7.2
 +
|The VirulenceFinder service contains one python script virulencefinder.py which is the script of the latest version of the VirulenceFinder service. VirulenceFinder identifies viruelnce genes in total or partial sequenced isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and Listeria are available.
 +
|-
 +
|[https://www.ks.uiuc.edu/Research/vmd/ VMD]
 +
|1.9.3-IGB-gcc-4.9.4<br>1.9.4a38-IGB-gcc-8.2.0
 +
|VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.  
 
|-
 
|-
−
|[http://bioinformatics.net.au/software.velvetoptimiser.shtml VelvetOptimiser]
+
|[https://github.com/torognes/vsearch VSEARCH]
−
|2.2.5
+
|2.4.3-IGB-gcc-4.9.4
−
|VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
+
|VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. - Homepage: https://github.com/torognes/vsearch
 
|-
 
|-
−
|[http://www.tbi.univie.ac.at/RNA/ ViennaRNA]
+
|[https://weblogo.threeplusone.com/ weblogo]
−
|2.1.9
+
|3.7.12-IGB-gcc-8.2.0-Python-3.10.1
−
|The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
+
|WebLogo is a web-based application designed to make the generation of sequence logos easy and painless. WebLogo has been featured in over 10000 scientific publications.  
 
|-
 
|-
−
|[http://vim.org vim]
+
|[https://github.com/whatshap/whatshap whatshap]
−
|7.4
+
|1.0-IGB-gcc-8.2.0-Python-3.7.2
−
|Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set. It's useful whether you're already using vi or using a different editor.
+
|WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
 
|-
 
|-
−
|[https://github.com/simroux/VirSorter virsorter]
+
|[http://didgeridoo.une.edu.au/km/wombat.php wombat]
−
|1.0.3
+
|20210107
−
|VIRSorter is a pipeline designed to mine microbial draft genomes for viral signal (complete viral contigs or viral regions within microbial contigs)
+
|WOMBAT is a program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML).
 
|-
 
|-
−
|virushunting
+
|[https://github.com/ruanjue/wtdbg2 wtdbg2]
−
|0.1, 0.2, 0.3, 0.4
+
|2.3-IGB-gcc-4.9.4<br>2.5-IGB-gcc-4.9.4
−
|Virus Hunting Pipeline Homepage:
+
|Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.
 
|-
 
|-
−
|[https://github.com/torognes/vsearch vsearch]
+
|[https://www.wxpython.org/ wxPython]
−
|1.0.7, 2.0.4, 2.4.0
+
|4.1.0-IGB-gcc-4.9.4-Python-3.6.1<br>4.1.0-IGB-gcc-8.2.0-Python-3.7.2
−
|VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed.
+
|the cross-platform GUI toolkit for the Python language. With wxPython software developers can create truly native user interfaces for their Python applications, that run with little or no modifications on Windows, Macs and Linux or other unix-like systems.  
 
|-
 
|-
−
|[http://bioen-compbio.bioen.illinois.edu/weaver/ weaver]
+
|x264
−
|0.20
+
|
−
|Allele specific base-pair resolution quantification of Strcutrual variations in cancer genome
+
|x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
 +
|-
 +
|[https://github.com/dmlc/xgboost xgboost]
 +
|0.80-IGB-gcc-4.9.4-Python-3.6.1
 +
|XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. It implements machine learning algorithms under the Gradient Boosting framework.
 +
|-
 +
|xorg-macros
 +
|
 +
|X.org macros utilities.
 
|-
 
|-
−
|[http://weblogo.threeplusone.com/manual.html weblogo]
+
|[https://xpore.readthedocs.io/en/latest/index.html xpore]
−
|2.8.2, 3.3
+
|2.1-IGB-gcc-8.2.0-Python-3.10.1
−
|WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.
+
|xPore is a Python package for identification of differentail RNA modifications from Nanopore sequencing data.
 
|-
 
|-
−
|[http://www.ncbi.nlm.nih.gov/pubmed/23413434 wessim]
+
|[https://github.com/parklab/xTea xTea]
−
|1.0
+
|0.1.6
−
|A whole-exome sequencing simulator based on in silico exome capture
+
|xTea (comprehensive transposable element analyzer) is designed to identify TE insertions from paired-end Illumina reads, barcode linked-reads, long reads (PacBio or Nanopore), or hybrid data from different sequencing platforms and takes whole-exome sequencing (WES) or whole-genome sequencing (WGS) data as input.
 
|-
 
|-
−
|[https://www.ebi.ac.uk/Tools/sss/fasta/wgs.html wgs]
+
|[http://tukaani.org/xz/ XZ]
−
|7.0
+
|5.2.3-IGB-gcc-4.9.4<br>5.2.3-IGB-gcc-8.2.0
−
|This tool provides sequence similarity searching against the EMBL (WGS) database using the FASTA suite of programs.
+
|xz: XZ utilities
 
|-
 
|-
−
|[https://wiki.gacrc.uga.edu/wiki/WISE2 wise]
+
|[https://github.com/c-zhou/yahs yahs]
−
|2.2.3-rc7
+
|1.2a.2-IGB-gcc-8.2.0
−
|Wise2 has four main executable programs using sequence inputs which are designed to provide access to the main algorithms sensibly. The algorithms you are interested in is genewise - compare protein information to genomic DNA and estwise - compare protein information to EST/cDNA DNA.
+
|YaHS is a scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies.
 
|-
 
|-
−
|[http://bioinformatics.research.nicta.com.au/software/xenome/ xenome]
+
|Yasm
−
|1.0.1-r
+
|
−
|A tool for classifying reads from xenograft samples.  Xenograft sequencing has many associated difficulties. Shotgun sequence read data derived from xenograft material contains a mixture of reads arising from the host and reads arising from the graft. Xenome is an application for classifying the read mixture to separate the two, allowing for more precise analysis to be performed.
+
|Yasm: Complete rewrite of the NASM assembler with BSD license
 
|-
 
|-
−
|[http://xerces.apache.org/ xerces-c]
+
|ZeroMQ
−
|3.1.2
+
|
−
|Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents. Xerces-C++ is faithful to the XML 1.0 and 1.1 recommendations and many associated standards.
+
|ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It is fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.
 
|-
 
|-
−
|[http://tukaani.org/xz/ xz]
+
|zlib
−
|5.2.2
+
|
−
|XZ Utils is free general-purpose data compression software with a high compression ratio. XZ Utils were written for POSIX-like systems, but also work on some not-so-POSIX systems. XZ Utils are the successor to LZMA Utils.
+
|zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
 
|-
 
|-
−
|[http://yasm.tortall.net/ yasm]
+
|[https://sourceforge.net/projects/probmask/files/ zorro]
−
|1.2.0
+
|20111201
−
|Yasm is a complete rewrite of the NASM assembler under the 'new' BSD License (some portions are under other licenses, see COPYING for details).  Yasm currently supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes, outputs binary, ELF32, ELF64, 32 and 64-bit Mach-O, RDOFF2, COFF, Win32, and Win64 object formats, and generates source debugging information in STABS, DWARF 2, and CodeView 8 formats
+
|A probabilistic alignment masking program
 
|-
 
|-
−
|[http://www.zlib.net/ zlib]
+
|[https://facebook.github.io/zstd zstd]
−
|1.2.8
+
|1.4.4-IGB-gcc-4.9.4<br>1.5.5-IGB-gcc-8.2.0
−
|zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. The zlib data format is itself portable across platforms.
+
|Zstandard is a real-time compression algorithm, providing high compression ratios.  It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.
 
|}
 
|}

Latest revision as of 04:00, 26 April 2024

Application Installed Versions Description
3d-dna 20190801-IGB-gcc-8.2.0-Python-3.7.2 De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds
454 2.8 The GS Data Analysis Software package includes the tools to investigate complex genomic variation in samples including de novo assembly, reference guided alignment and variant calling, and low abundance variant identification and quantification. - Homepage: http://454.com/products/analysis-software/index.asp
a2ps 4.14-IGB-gcc-4.9.4
4.14-IGB-gcc-8.2.0 		a2ps-4.14: Formats an ascii file for printing on a postscript printer
abcranger 1.2.64 Random forests methodologies for ABC model choice and ABC Bayesian parameter inference (
Abseil 20230125.2-IGB-gcc-8.2.0
20230125.3-IGB-gcc-8.2.0 		Abseil is an open-source collection of C++ library code designed to augment theC++ standard library. The Abseil library code is collected from Google's ownC++ code base, has been extensively tested and used in production, and is thesame code we depend on in our daily coding lives.
ABySS 2.0.2-IGB-gcc-4.9.4 ABySS is a de novo, parallel, paired-end sequence assembler that is designed for short reads. The single-processor version is useful for assembling genomes up to 100 Mbases in size. The parallel version is implemented using MPI and is capable of assembling larger genomes.
abyss 2.2.5-IGB-gcc-8.2.0 ABySS is a de novo sequence assembler intended for short paired-end reads and large genomes.
AdapterRemoval 2.1.7-IGB-gcc-4.9.4 This program searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3 end of reads following adapter removal.
AdmixTools 1.0.1-IGB-gcc-4.9.4 The ADMIXTOOLS package implements 5 methods described in Patterson et al. (2012) Ancient Admixture in Human History. Details of the methods and algorithm can be found in this paper.
admixture 1.3.0 ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm.
ADOL-C 2.6.3-IGB-gcc-4.9.4 ADOL-C is an open-source package for the automatic differentiation of C and C++ programs.
AGAT 0.5.1-IGB-gcc-8.2.0-Perl-5.28.1 Suite of tools to handle gene annotations in any GTF/GFF format.
AGEnt 0.2.1-IGB-gcc-4.9.4 AGEnt performs in silico subtractive hybridization of core genome sequences, such as those produced by Spine, against a query genomic sequence to identify accessory genomic sequences (AGEs) in the query genome. Sequences are aligned using Nucmer, outputting sequences and sequence characteristics of those regions in the query genome that are not found in the core genome. If gene coordinate information is provided, a list of accessory genes in the query genome will also be output.
albacore 2.0.2-IGB-gcc-4.9.4-Python-3.6.1
2.1.10-IGB-gcc-4.9.4-Python-3.6.1
2.3.1-IGB-gcc-4.9.4-Python-3.6.1 		Local basecalling for MinKNOW
alevin-fry 0.4.2 alevin-fry is a suite of tools for the rapid, accurate and memory-frugal processing single-cell and single-nucleus sequencing data.
alfa 1.1.1-IGB-gcc-8.2.0-Python-3.7.2 ALFA provides a global overview of features distribution composing NGS dataset(s).
AlignGraph 20180222-IGB-gcc-4.9.4 AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism.
alphafold 2.1.2
2.3.1
2.3.2 		This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document.
AMOS 3.1.0-IGB-gcc-4.9.4 The AMOS consortium is committed to the development of open-source whole genome assembly software.
AMPHORA2 20190104-IGB-gcc-4.9.4 An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
Anacapa 20200814-IGB-gcc-4.9.4-Python-2.7.13 Anacapa is an eDNA toolkit that allows users to build comprehensive reference databases and assign taxonomy to raw multilocus metabarcode sequence data.
Anaconda2 4.3.1 Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. - Homepage: https://www.continuum.io/anaconda-overview
Anaconda3 2019.10
2022.05
2023.09
5.0.1
5.1.0 		Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
ANGSD 0.933-IGB-gcc-4.9.4
0.941-IGB-gcc-8.2.0 		ANGSD is a software for analyzing next generation sequencing data. The software can handle a number of different input types from mapped reads to imputed genotype probabilities.
ANIcalculator 1.0
ANNOVAR 2019Oct24-IGB-gcc-8.2.0-Perl-5.28.1 ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others).
ant 1.10.1-Java-1.8.0_121
1.10.1-Java-1.8.0_152
1.10.10-Java-15.0.1
1.10.13-Java-15.0.1
1.10.9-Java-1.8.0_201 		Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
antismash 4.1.0
5.1.2
6.1.0 		antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. It integrates and cross-links with a large number of in silico secondary metabolite analysis tools that have been published earlier.
ANTLR ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions.
anvio 5.5-IGB-gcc-4.9.4-Python-3.6.1
6.1-IGB-gcc-4.9.4-Python-3.6.1
7.1-IGB-gcc-4.9.4-Python-3.6.1 		Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.
any2fasta 0.4.2-IGB-gcc-8.2.0-Perl-5.28.1 Convert various sequence formats to FASTA
apollo 20200510-IGB-gcc-8.2.0 A Sequencing-Technology-Independent, Scalable, and Accurate Assembly Polishing Algorithm
ARB 6.0.6 The ARB software is a graphically oriented package comprising various tools for sequence database handling and data analysis. A central database of processed (aligned) sequences and any type of additional data linked to the respective sequence entries is structured according to phylogeny or other user defined criteria
ArcadeLearningEnvironment 0.5.1-IGB-gcc-4.9.4-Python-2.7.13 The Arcade Learning Environment (ALE) -- a platform for AI research. - Homepage: https://github.com/mgbellemare/Arcade-Learning-Environment
ARCS 1.0.0-IGB-gcc-4.9.4-Perl-5.24.1
1.2.1-IGB-gcc-8.2.0-Perl-5.28.1 		Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data.
argtable Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.
aria2 1.36.0-IGB-gcc-8.2.0
1.37.0-IGB-gcc-8.2.0 		aria2 is a lightweight multi-protocol & multi-source command-line download utility.
Arlequin 3.5 An Integrated Software for Population Genetics Data Analysis
ASEr 0.2-IGB-gcc-8.2.0-Python-3.7.2 Get ASE counts from BAMs or raw fastq data
aspera 3.7.6
4.2.7.445 		Aspera’s unwavering mission is to create the next-generation software technologies that move the world’s data at maximum speed, regardless of file size, transfer distance and network conditions.
Assemblytics 3f570cd-IGB-gcc-4.9.4
df5361f-IGB-gcc-4.9.4 		Analyze your assembly by comparing it to a reference genome
asset 1.0.3-IGB-gcc-8.2.0 Assembly evaluation tool
atactk 0.1.6-IGB-gcc-4.9.4-Python-2.7.13 a toolkit for ATAC-seq data
ATK ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.
AUGUSTUS 3.3-IGB-gcc-4.9.4 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
augustus 3.2.3-IGB-gcc-4.9.4
3.3.2-IGB-gcc-4.9.4
3.3.3-IGB-gcc-8.2.0
3.4.0-IGB-gcc-8.2.0 		AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
Autoconf Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. - Homepage: http://www.gnu.org/software/autoconf/
Automake Automake: GNU Standards-compliant Makefile generator
Autotools This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
awkde 20220617-IGB-gcc-8.2.0-Python-3.7.2 This uses the awesome pybind11 package which makes creating C++ bindings super convenient. Only the evaluation is written in a small C++ snippet to speed it up, the rest is a pure python implementation.
awscli 1.16.113-IGB-gcc-4.9.4-Python-3.6.1
1.18.96-IGB-gcc-8.2.0-Python-3.7.2 		The AWS Command Line Interface (CLI) is a unified tool to manage your AWS services. With just one tool to download and configure, you can control multiple AWS services from the command line and automate them through scripts.
bam-readcount 0.8.0-IGB-gcc-4.9.4 The purpose of this program is to generate metrics at single nucleotide positions.
BamM 1.7.3-IGB-gcc-4.9.4-Python-2.7.13 The primary motivation for building BamM was to replaace PySam in GroopM. Not saying PySam is bad, it's just that GroopM doesn't need all the PySam features and what it does need can be done way way faster in C-land.
bamm-suite 20191127-IGB-gcc-4.9.4-Python-3.6.1 BaMM-suite is the motif finding suite developed by the Soedinglab.
bammds 20140602-IGB-gcc-4.9.4 Software that allows to create a multidimensional scaling (MDS) plot of populations for genetic data.
BaMMmotif 2.0 Bayesian Markov Model motif discovery software (version 2).
BamTools 2.4.1-IGB-gcc-4.9.4
2.5.1-IGB-gcc-4.9.4
2.5.1-IGB-gcc-8.2.0 		BamTools provides both a programmers API and an end-users toolkit for handling BAM files.
barrnap 0.9-IGB-gcc-4.9.4 Barrnap predicts the location of ribosomal RNA genes in genomes.
bart2 20240302-IGB-gcc-8.2.0-Python-3.7.2 BART (Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcriptional regulators (TRs) that bind at genomic cis-regulatory regions to regulate gene expression in the human or mouse genomes, taking a query gene set, a ChIP-seq dataset or a scored genomic region set as input.
basespace-cli 1.5.1 You can work with your BaseSpace Sequence Hub data using the command line interface (CLI). The BaseSpace Sequence Hub CLI supports scripting and programmatic access to BaseSpace Sequence Hub for automation, bulk operations, and other routine functions. It can be used independently or in conjunction with BaseMount.
bax2bam 20171114-IGB-gcc-4.9.4 bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAMbasecall format.
BayeScan 2.1 This program, BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. BayeScan is based on the multinomial-Dirichlet model.
bazel 0.6.0-Java-1.8.0_121 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Googles software.
BBMap 38.36-Java-1.8.0_152
38.94-Java-1.8.0_201 		BBMap short read aligner, and other bioinformatic tools.
BCFtools 1.12-IGB-gcc-8.2.0
1.17-IGB-gcc-8.2.0
1.4-IGB-gcc-4.9.4
1.5-IGB-gcc-4.9.4
1.7-IGB-gcc-4.9.4
1.9-IGB-gcc-4.9.4 		BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF
bcl 4.0.0
bcl2fastq2 2.20
2.20-IGB-gcc-8.2.0 		The bcl2fastq2 Conversion Software v2.20.0 can be used to convert BCL files from MiniSeq, MiSeq, NextSeq, HiSeq, and NovaSeq sequening systems. For conversion of data generated on Illumina sequencing systems using versions of RTA earlier than RTA 1.18.54, use bcl2fastq v1.8.4.
beagle 03Jul18.40b-Java-1.8.0_152
5.1-Java-1.8.0_152 		Beagle is a software package for phasing genotypes and for imputing ungenotyped markers. Version 5.0 has new, fast algorithms for genotype phasing and imputation.
beagle-lib 4.0.0-IGB-gcc-8.2.0 BEAGLE is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. It can make use of highly-parallel processors such as those in graphics cards (GPUs) found in many PCs.
BEAST2 2.7.5-IGB-gcc-8.2.0 BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models.
beast2 2.6.7-Java-1.8.0_201 BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences. It estimates rooted, time-measured phylogenies using strict or relaxed molecular clock models.
bedops 2.4.30 BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
BEDTools 2.21.0-IGB-gcc-4.9.4
2.26.0-IGB-gcc-4.9.4
2.28.0-IGB-gcc-8.2.0 		The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
Bifrost 1.0.4-IGB-gcc-8.2.0 Parallel construction, indexing and querying of colored and compacted de Bruijn graphs
big-map2-analyse 20200124 This is the Github repository for the Biosynthetic Gene cluster Meta’omics abundance Profiler
big-map2-process 20200124 This is the Github repository for the Biosynthetic Gene cluster Meta’omics abundance Profiler
BiG-SCAPE 1.0.1-IGB-gcc-4.9.4-Python-3.6.1
1.1.5-IGB-gcc-8.2.0-Python-3.7.2 		BiG-SCAPE (Biosynthetic Gene Similarity Clustering and Prospecting Engine) is a software package, written in Python, that constructs sequence similarity networks of Biosynthetic Gene Clusters (BGCs) and groups them into Gene Cluster Families (GCFs)
binutils binutils: GNU binary utilities
bio-embeddings 0.2.2-IGB-gcc-8.2.0-Python-3.7.2 Quickly predict protein structure and function from sequence via embeddings:
bio-rocker 1.2.0-IGB-gcc-4.9.4-Ruby-2.4.2 Accurately detecting functional genes in metagenomes.
bioawk 1.0-IGB-gcc-8.2.0 Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
biodatabase 1.0-IGB-gcc-4.9.4 Scripts to create databases on the biodatabase machine.
biom-format 2.1.6-IGB-gcc-4.9.4-Python-2.7.13
2.1.6-IGB-gcc-4.9.4-Python-3.6.1
2.1.8-IGB-gcc-4.9.4-Python-3.6.1
2.1.8-IGB-gcc-8.2.0-Python-3.7.2 		The BIOM file format (canonically pronounced biome) is designed to be a general-useformat for representing biological sample by observation contingency tables.
BioPerl 1.7.1-IGB-gcc-4.9.4-Perl-5.24.1
1.7.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
1.7.2-IGB-gcc-8.2.0-Perl-5.28.1 		Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
Biopieces 2.0-IGB-gcc-4.9.4-Perl-5.24.1 Biopieces is a bioinformatic framework of tools easily used and easily created.
Biopython 1.68-IGB-gcc-4.9.4-Python-2.7.13
1.68-IGB-gcc-4.9.4-Python-3.6.1
1.76-IGB-gcc-4.9.4-Python-3.6.1
1.76-IGB-gcc-8.2.0-Python-3.7.2
1.79-IGB-gcc-8.2.0-Python-3.7.2
1.83-IGB-gcc-8.2.0-Python-3.10.1 		Biopython is a set of freely available tools for biological computation writtenin Python by an international team of developers. It is a distributed collaborative effort todevelop Python libraries and applications which address the needs of current and future work inbioinformatics.
bioservices 1.7.9-IGB-gcc-4.9.4-Python-3.6.1 Bioservices is a Python package that provides access to many Bioinformatices Web Services (e.g., UniProt) and a framework to easily implement Web Services wrappers (based on WSDL/SOAP or REST protocols).
Bismark 0.17.0-IGB-gcc-4.9.4-Perl-5.24.1
0.18.1-IGB-gcc-4.9.4-Perl-5.24.1
0.22.1-IGB-gcc-4.9.4-Perl-5.24.1
0.22.3-IGB-gcc-8.2.0-Perl-5.28.1 		A tool to map bisulfite converted sequence reads and determine cytosine methylation states
Bison Bison is a general-purpose parser generator that converts an annotated context-free grammarinto a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.
BLASR 4.0.0-IGB-gcc-4.9.4 BLASR (Basic Local Alignment with Successive Refinement) rapidly maps reads to genomes by finding the highest scoring local alignment or set of local alignments between the read and the genome. Optimized for PacBios extraordinarily long reads and taking advantage of rich quality values, BLASR maps reads rapidly with high accuracy.
BLAST 2.2.26-Linux_x86_64 Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
BLAST+ 2.10.1-IGB-gcc-8.2.0
2.13.0-IGB-gcc-8.2.0
2.2.31-IGB-gcc-4.9.4
2.6.0-IGB-gcc-4.9.4
2.7.1-IGB-gcc-4.9.4
2.9.0-IGB-gcc-4.9.4 		Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
BLAT 3.5-IGB-gcc-4.9.4 BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
blobtools 0.9.19.6-IGB-gcc-4.9.4-Python-2.7.13
1.0.1-IGB-gcc-4.9.4-Python-2.7.13
1.1.1-IGB-gcc-4.9.4-Python-3.6.1 		Application for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots
blobtools2 2.6.1-IGB-gcc-4.9.4-Python-3.6.1
2.6.4-IGB-gcc-8.2.0-Python-3.7.2 		Application for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots
bnpm v7.20.0-IGB-gcc-4.9.4 the package manager for JavaScript
Boost Boost provides free peer-reviewed portable C++ source libraries.
Boost.Python Boost provides free peer-reviewed portable C++ source libraries.
Bowtie 1.1.2-IGB-gcc-4.9.4
1.2.0-IGB-gcc-4.9.4
1.2.2-IGB-gcc-4.9.4
1.3.0-IGB-gcc-8.2.0 		Bowtie is an ultrafast, memory-efficient short read aligner.It aligns short DNA sequences (reads) to the human genome.
Bowtie2 2.1.0-IGB-gcc-4.9.4
2.3.1-IGB-gcc-4.9.4
2.3.2-IGB-gcc-4.9.4
2.3.5.1-IGB-gcc-4.9.4
2.4.1-IGB-gcc-8.2.0
2.4.2-IGB-gcc-8.2.0
2.4.5-IGB-gcc-8.2.0
2.5.3-IGB-gcc-8.2.0 		Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
Bracken 2.6.2-IGB-gcc-4.9.4
2.6.2-IGB-gcc-8.2.0 		Bracken is a companion program to Kraken 1 or Kraken 2 While Kraken classifies reads to multiple levels in the taxonomic tree, Bracken allows estimation of abundance at a single level using those classifications (e.g. Bracken can estimate abundance of species within a sample).
BRAKER 2.1.2-IGB-gcc-4.9.4
2.1.5-IGB-gcc-4.9.4
2.1.5-IGB-gcc-8.2.0
2.1.6-IGB-gcc-8.2.0
3.0.3-IGB-gcc-8.2.0 		BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
BreakSeq2 2.2-IGB-gcc-4.9.4-Python-2.7.13 Ultrafast and accurate nucleotide-resolution analysis of structural variants - Homepage: http://bioinform.github.io/breakseq2/
breseq 0.31.0-IGB-gcc-4.9.4
0.36.1-IGB-gcc-8.2.0
0.37.0-IGB-gcc-8.2.0 		is a computational pipeline for the analysis of short-read re-sequencing data (e.g. Illumina, 454, IonTorrent, etc.). It uses reference-based alignment approaches to predict mutations in a sample relative to an already sequenced genome.
BRIG 0.95-Java-1.8.0_152 BRIG is a free cross-platform (Windows/Mac/Unix) application that can display circular comparisons between a large number of genomes, with a focus on handling genome assembly data.
BS-Seeker 2.1.2-IGB-gcc-4.9.4-Python-2.7.13 BS Seeker 2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated short reads.
BS-Snper 20170222-IGB-gcc-4.9.4-Perl-5.24.1 BS-SNPer is an ultrafast and memory-efficient package, a program for BS-Seq variation detection from alignments in standard BAM/SAM format using approximate Bayesian modeling.
BUSCO 3.0.1-IGB-gcc-4.9.4-Python-2.7.13
4.1.4-IGB-gcc-8.2.0-Python-3.7.2
5.1.2-IGB-gcc-8.2.0-Python-3.7.2
5.3.2-IGB-gcc-8.2.0-Python-3.7.2
5.4.4-IGB-gcc-8.2.0-Python-3.7.2
5.5.0-IGB-gcc-8.2.0-Python-3.7.2 		Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs (BUSCO)
BWA 0.5.9-IGB-gcc-4.9.4
0.6.2-IGB-gcc-4.9.4
0.7.15-IGB-gcc-4.9.4
0.7.17-IGB-gcc-4.9.4
0.7.17-IGB-gcc-8.2.0 		Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
bx-python 0.8.13-IGB-gcc-8.2.0-Python-3.7.2 The bx-python project is a Python library and associated set of scripts for rapid implementation of genome scale analyses.
byacc 20170709-IGB-gcc-4.9.4 Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available.In contrast to bison, it is written to avoid dependencies upon a particular compiler.
bzip2 1.0.6-IGB-gcc-4.9.4
1.0.6-IGB-gcc-8.2.0 		bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.
c-ares c-ares is a C library for asynchronous DNS requests (including name resolves)
cactus 20180705-IGB-gcc-4.9.4-Python-2.7.13 Cactus is a reference-free whole-genome multiple alignment program.
cairo Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
Canu 1.4-IGB-gcc-4.9.4-Perl-5.24.1
1.5-IGB-gcc-4.9.4-Perl-5.24.1
1.6-IGB-gcc-4.9.4-Perl-5.24.1
1.7-IGB-gcc-4.9.4-Perl-5.24.1
1.7.1-IGB-gcc-4.9.4-Perl-5.24.1
1.8-IGB-gcc-4.9.4-Perl-5.24.1
1.9-IGB-gcc-8.2.0-Perl-5.28.1
2.0-IGB-gcc-8.2.0-Perl-5.28.1
2.1.1-IGB-gcc-8.2.0-Perl-5.28.1
2.2-IGB-gcc-8.2.0-Perl-5.28.1 		Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II or Oxford Nanopore MinION).
cap-mirseq 20200817-IGB-gcc-4.9.4 CAP-miRSeq: A comprehensive analysis pipeline for deep microRNA sequencing
capnproto Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. Think JSON, except binary. Or think Protocol Buffers, except faster.
cbc_pacbio beta-IGB-gcc-8.2.0 Command-line scripts and pipelines to perform downstream analyses of Sequel II subreads
CCMpred 20191102-IGB-gcc-4.9.4 CCMpred is a C implementation of a Markov Random Field pseudo-likelihood maximization for learning protein residue-residue contacts as made popular by Ekeberg et al. [1] and Balakrishnan and Kamisetty [2].
CD-HIT 4.6.6-IGB-gcc-4.9.4
4.8.1-IGB-gcc-8.2.0 		CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
cdbfasta 20170316-IGB-gcc-4.9.4
20181005-IGB-gcc-8.2.0 		CDB (Constant DataBase) indexing and retrieval tools for FASTA files
cddd 20200130-IGB-gcc-4.9.4-Python-3.6.1 Continuous and Data-Driven Descriptors
cellranger 2.1.0
2.1.1
3.0.0
3.0.1
3.1.0
4.0.0
5.0.0
6.0.1
6.0.2
6.1.1
7.0.0
7.0.1
7.1.0
7.2.0
8.0.0 		Cell Ranger is a set of analysis pipelines that process Chromium single cell 3 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
cellranger-arc 1.0.0
2.0.1
2.0.2 		Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage.
cellranger-atac 1.1.0
1.2.0
2.0.0
2.1.0 		Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.
centrifuge 1.0.3-beta-IGB-gcc-4.9.4
1.0.4-beta-IGB-gcc-4.9.4 		Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems.
ceres-solver 1.14.0-IGB-gcc-4.9.4
1.14.0-IGB-gcc-8.2.0
2.0.0-IGB-gcc-8.2.0 		Ceres Solver is an open source C++ library for modeling and solving large, complicated optimization problems.
CheckM 1.0.7-IGB-gcc-4.9.4-Python-2.7.13
1.1.3-IGB-gcc-8.2.0-Python-3.7.2
1.1.9-IGB-gcc-8.2.0-Python-3.7.2 		CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
CheckM2 1.0.1 Unlike CheckM1, CheckM2 has universally trained machine learning models it applies regardless of taxonomic lineage to predict the completeness and contamination of genomic bins.
chopchop 20190211-IGB-gcc-4.9.4-Python-2.7.13 CHOPCHOP is a python script that allows quick and customizable design of guide RNA. We support selecting target sites for CRISPR/Cas9, CRISPR/Cpf1 or TALEN with wide range of customization. We even support C2c2 for isoform targeting.
Chromonomer 1.13-IGB-gcc-8.2.0 Chromonomer is a program designed to integrate a genome assembly with a genetic map. Chromonomer tries very hard to identify and remove markers that are out of order in the genetic map, when considered against their local assembly order; and to identify scaffolds that have been incorrectly assembled according to the genetic map, and split those scaffolds.
Circlator 1.5.1-IGB-gcc-4.9.4-Python-3.6.1
1.5.5-IGB-gcc-8.2.0-Python-3.7.2 		A tool to circularize genome assemblies.
Circos 0.69-4-IGB-gcc-4.9.4-Perl-5.24.1
0.69-9-IGB-gcc-8.2.0-Perl-5.28.1 		Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.
cisgenome 2.0-IGB-gcc-4.9.4 An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
clang-format 15.0.7-IGB-gcc-8.2.0-Python-3.7.2 Clang-Format is an LLVM-based code formatting tool
CLASS2 2.1.7-IGB-gcc-8.2.0 CLASS2 is a fast and accurate program for transcript assembly of RNA-seq reads aligned to a reference genome. CLASS2 uses the splice graph model to represent a gene and its splice variants, and a dynamic programming optimization algorithm to score and select a subset of transcripts most likely present in the sample.
clinker 0.0.27-IGB-gcc-8.2.0-Python-3.7.2 clinker is a pipeline for easily generating publication-quality gene cluster comparison figures.
clipper 1.2.1-IGB-gcc-4.9.4-Python-2.7.13 A tool to detect CLIP-seq peaks.
Clp Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.
CLUMPP 1.1.2 CLUMPP is a program that deals with label switching and multimodality problems in population-genetic cluster analyses.
Clustal-Omega 1.2.4-IGB-gcc-4.9.4
1.2.4-IGB-gcc-8.2.0 		Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms
ClustalW2 2.1-IGB-gcc-4.9.4 ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. - Homepage: http://www.ebi.ac.uk/Tools/msa/clustalw2/
clusterflow 0.5-IGB-gcc-4.9.4-Perl-5.24.1 Cluster Flow is workflow manager designed to run bioinformatics pipelines. It is operated through a single command cf, which can be used to launch, configure, monitor and cancel pipelines.
CMake CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
CNVkit 0.9.10-IGB-gcc-8.2.0-Python-3.10.1
0.9.8-IGB-gcc-8.2.0-Python-3.7.2 		A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
CNVnator 0.3.3-IGB-gcc-4.9.4
0.3.3-IGB-gcc-4.9.4-Python-2.7.13 		a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
cocoapi 20190218-IGB-gcc-4.9.4-Python-3.6.1 OCO is a large image dataset designed for object detection, segmentation, person keypoints detection, stuff segmentation, and caption generation.
colmap 20210330-IGB-gcc-4.9.4 COLMAP is a general-purpose Structure-from-Motion (SfM) and Multi-View Stereo (MVS) pipeline with a graphical and command-line interface. It offers a wide range of features for reconstruction of ordered and unordered image collections.
CONCOCT 1.0.0-IGB-gcc-4.9.4-Python-3.6.1
1.1.0-IGB-gcc-8.2.0-Python-3.7.2 		A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
cooler 0.8.11-IGB-gcc-8.2.0-Python-3.7.2
0.8.2-IGB-gcc-8.2.0-Python-3.7.2 		Cooler is a support library for a sparse, compressed, binary persistent storage format, also called cooler, used to store genomic interaction data, such as Hi-C contact matrices.
cooltools 0.4.1-IGB-gcc-8.2.0-Python-3.7.2 The tools for your .cools
COPIES 20231202-IGB-gcc-8.2.0-Python-3.10.1 COmputational Pipeline for the Identification of CRISPR/Cas-facilitated intEgration Sites (CRISPR-COPIES) is a user-friendly web application and a command line tool for rapid discovery of neutral integration sites.
coreutils 8.28-IGB-gcc-4.9.4
8.28-IGB-gcc-8.2.0
9.1-IGB-gcc-8.2.0 		The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system.These are the core utilities which are expected to exist on every operating system.
cortex 1.0.5.21-IGB-gcc-4.9.4 reference free variant assembly
CppUnit CppUnit is the C++ port of the famous JUnit framework for unit testing.
crb-blast 0.6.9-IGB-gcc-4.9.4 Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation.
crimap 2.507-IGB-gcc-8.2.0 CRI-MAP (version 2.4, by Phil Green et al, 1990) has been used extensively in the past 20 years for genetic linkage analysis of diploid species, and has played a fundamental role in producing genetic linkage maps for humans, rats, mouse, fruit flies, cattle, sheep, pigs, chicken, fish, among many other species.
cromwell 39-Java-1.8.0_152 Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Crossmap 0.6.5-IGB-gcc-8.2.0-Python-3.7.2 CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF, MAF VCF, and gVCF.
CUDA 10.0.130
10.1.105
11.0.3
11.1.0
11.2.2
11.3.0
11.8.0
8.0.61
8.0.61-IGB-gcc-4.9.4
9.0.176
9.1.85 		CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
cuDNN 5.1-CUDA-8.0.61
5.1-IGB-gcc-4.9.4-CUDA-8.0.61
6.0-IGB-gcc-4.9.4-CUDA-8.0.61
7.0.5-CUDA-9.0.176
7.1.4-CUDA-9.0.176
7.6.1.34-CUDA-10.0.130
8.0.4.30-CUDA-10.1.105
8.0.4.30-CUDA-11.1.0
8.1.1.33-CUDA-11.2.2
8.2.1.32-CUDA-11.3.0
8.9.2.23-CUDA-11.8.0 		The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
Cufflinks 2.2.1
2.2.1-IGB-gcc-4.9.4-b4fa050 		Transcript assembly, differential expression, and differential regulation for RNA-Seq
CUnit 2.1-3-IGB-gcc-4.9.4 CUnit is a lightweight system for writing, administering, and running unit tests in C. It provides C programmers a basic testing functionality with a flexible variety of user interfaces.
cURL libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.
cutadapt 1.14-IGB-gcc-4.9.4-Python-2.7.13
1.17-IGB-gcc-4.9.4-Python-3.6.1
2.10-IGB-gcc-8.2.0-Python-3.7.2
3.7-IGB-gcc-8.2.0-Python-3.7.2 		Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cuteSV 1.0.12-IGB-gcc-8.2.0-Python-3.7.2 A sensitive, fast and scalable long-read-based SV detection approach. cuteSV uses tailored methods to collect the signatures of various types of SVs and employs a clustering-and-refinement method to analyze the signatures to implement sensitive SV detection.
cytoscape 3.7.0-Java-1.8.0_152
3.8.2-Java-11.0.5
3.9.1-Java-11.0.5 		Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
damidseq 1.4-IGB-gcc-4.9.4 Processing DamID-seq data involves extending single-end reads, aligning the reads to the genome and determining the coverage, similar to processing regular ChIP-seq datasets.
DamMet 1.0.2-IGB-gcc-8.2.0 DamMet is probabilistic model for mapping ancient methylomes using sequencing data underlying an ancient specimen.
DANPOS 2.2.2-IGB-gcc-4.9.4-Python-2.7.13-R-3.3.3 A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2
DAS_Tool 1.1.2-IGB-gcc-4.9.4 DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly.
DB 18.1.32-IGB-gcc-4.9.4 Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
DeepEC 20190806-IGB-gcc-4.9.4-Python-3.6.1 DeepEC
deeplabcut 2.1.8.2-IGB-gcc-4.9.4-Python-3.6.1
2.2.1.1-IGB-gcc-8.2.0-Python-3.7.2 		Markerless pose estimation of user-defined features with deep learning for all animals
deepTools 2.5.3-IGB-gcc-4.9.4-Python-2.7.13
3.0.1-IGB-gcc-4.9.4-Python-2.7.13
3.2.1-IGB-gcc-4.9.4-Python-3.6.1
3.5.2-IGB-gcc-4.9.4-Python-3.6.1
3.5.2-IGB-gcc-8.2.0-Python-3.7.2 		deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome.
deep_q_rl 20160603-IGB-gcc-4.9.4-Python-2.7.13 This package provides a Lasagne/Theano-based implementation of the deep Q-learning algorithm described in:Playing Atari with Deep Reinforcement Learning Volodymyr Mnih, Koray Kavukcuoglu, David Silver, Alex Graves, Ioannis Antonoglou, Daan Wierstra, Martin RiedmillerandMnih, Volodymyr, et al. "Human-level control through deep reinforcement learning." Nature 518.7540 (2015): 529-533.
delly 0.8.1-IGB-gcc-4.9.4 Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data.
DendroPy 4.4.0-IGB-gcc-4.9.4-Python-3.6.1
4.4.0-IGB-gcc-8.2.0-Python-3.7.2 		DendroPy is a Python library for phylogenetic computing.
deNOPA 1.0.2-IGB-gcc-4.9.4-Python-2.7.13 As the basal bricks, the dynamics and arrangement of nucleosomes orchestrate the higher architecture of chromatin in a fundamental way, thereby affecting almost all nuclear biology processes.
detectron2 0.2.1-IGB-gcc-4.9.4-Python-3.6.1
0.2.1-IGB-gcc-8.2.0-Python-3.7.2
0.5-IGB-gcc-8.2.0-Python-3.7.2
0.6-IGB-gcc-8.2.0-Python-3.7.2 		Detectron2 is Facebook AI Research's next generation software system that implements state-of-the-art object detection algorithms
DIAMOND 0.8.38-IGB-gcc-4.9.4
0.9.10-IGB-gcc-4.9.4
0.9.16-IGB-gcc-4.9.4
0.9.22-IGB-gcc-4.9.4
0.9.24-IGB-gcc-4.9.4
0.9.24-IGB-gcc-8.2.0
0.9.36-IGB-gcc-8.2.0
0.9.9-IGB-gcc-4.9.4
2.0.15-IGB-gcc-8.2.0
2.0.6-IGB-gcc-8.2.0
2.0.9-IGB-gcc-8.2.0 		Accelerated BLAST compatible local sequence aligner
diffReps 1.55.6-IGB-gcc-4.9.4-Perl-5.24.1 ChIP-seq is now widely used to profile the protein DNA interactions on a genome. It is of high interest to compare the differential enrichment of a histone mark or transcription factor between two contrasting conditions, such as disease vs. control. diffReps is developed to serve this purpose. It scans the whole genome using a sliding window, performing millions of statistical tests and report the significant hits. - Homepage: https://github.com/shenlab-sinai/diffreps
DISCOVARdenovo 52488-IGB-gcc-4.9.4 DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.
distruct 2.2-IGB-gcc-4.9.4 Modified version of the original distruct.py
DIYABC 2.1.0 a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers
diyabc 1.1.28 DIYABC RF V1.0
dms-tools2 2.6.10-IGB-gcc-8.2.0-Python-3.7.2 dms_tools2 is a software package for analyzing deep mutational scanning data. It is tailored to analyze libraries created using comprehensive codon mutagenesis of protein-coding genes, and perform analyses that are common to the Bloom lab,
dorado 0.6.0 Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
Doxygen 1.8.13-IGB-gcc-4.9.4 Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.
drep 3.2.0-IGB-gcc-8.2.0-Python-3.7.2 dRep is a python program which performs rapid pair-wise comparison of genome sets. One of it’s major purposes is for genome de-replication, but it can do a lot more.
ds3_java_cli 5.1.2
5.1.4 		Command line utilities for Bioarchive
ea-utils 1.04.807-IGB-gcc-4.9.4 Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs.
EasyBuild 4.6.2 EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
EAT 1.0.0-IGB-gcc-8.2.0-Python-3.7.2 Embedding-based annotation transfer (EAT) uses Euclidean distance between vector representations (embeddings) of proteins to transfer annotations from a set of labeled lookup protein embeddings to query protein embeddings.
EDirect 20160310-IGB-gcc-4.9.4 Entrez Direct (EDirect) provides access to the NCBI's suite of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
eeglab 2021.1-IGB-gcc-8.2.0 EEGLAB is an interactive Matlab toolbox for processing continuous and event-related EEG, MEG and other electrophysiological data incorporating independent component analysis (ICA), time/frequency analysis, artifact rejection, event-related statistics, and several useful modes of visualization of the averaged and single-trial data.
eggnog-mapper 2.1.12-IGB-gcc-8.2.0-Python-3.7.2 EggNOG-mapper is a tool for fast functional annotation of novel sequences.
Eigen Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
eigensoft 7.2.1-IGB-gcc-4.9.4 The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006).
EMBOSS 6.6.0-IGB-gcc-4.9.4-Java-1.8.0_121 EMBOSS, The European Molecular Biology Open Software Suite. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
EMIRGE 0.61.1-IGB-gcc-4.9.4-Python-2.7.13 EMIRGE reconstructs full length ribosomal genes from short readsequencing data. In the process, it also provides estimates of thesequences abundances.
epa-ng 0.3.8-IGB-gcc-8.2.0 EPA-ng is a complete rewrite of the Evolutionary Placement Algorithm (EPA), previously implemented in RAxML. It uses libpll and pll-modules to perform maximum likelihood-based phylogenetic placement of genetic sequences on a user-supplied reference tree and alignment.
epic 0.2.9-IGB-gcc-4.9.4-Python-2.7.13 epic is a software package for finding medium to diffusely enriched domains in chip-seq data. It is a fast, parallel and memory-efficient implementation of the incredibly popular SICER algorithm.
epic2 0.0.41-IGB-gcc-4.9.4-Python-3.6.1 epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use.
EVidenceModeler 1.1.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
1.1.1-IGB-gcc-8.2.0-Perl-5.28.1 		The EVidenceModeler (aka EVM) software combines ab intio gene predictions and protein and transcript alignments into weighted consensus gene structures. EVM provides a flexible and intuitive framework for combining diverse evidence types into a single automated gene structure annotation system.
evolocity 0.1-IGB-gcc-8.2.0-Python-3.7.2 Evolocity is a Python package that implements evolutionary velocity, which constructs landscapes of protein evolution by using the local evolutionary predictions enabled by language models to predict the directionality of evolution and is described in the paper "Evolutionary velocity with protein language models" by Brian Hie, Kevin Yang, and Peter Kim.
exiftool 12.54-IGB-gcc-8.2.0-Perl-5.28.1 Read, Write and Edit Meta Information!
exonerate 2.2.0-IGB-gcc-4.9.4
2.2.0-IGB-gcc-8.2.0 		Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, either exhaustive dynamic programming or a variety of heuristics.
ExonOntology 20171018-IGB-gcc-8.2.0-Perl-5.28.1 This project consists of a set of scripts that are necessary to perform offline Exon Ontology analyses. Briefly, it can accept a list of genomic sequences as input that represent exons (or parts of exons). The algorithm then retrieves the protein features that are encoded by these DNA sequences.
expat Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)
fair-esm 0.4.0-IGB-gcc-8.2.0-Python-3.7.2
2.0.0-IGB-gcc-8.2.0-Python-3.7.2 		This repository contains code and pre-trained weights for Transformer protein language models from Facebook AI Research, including our state-of-the-art ESM-1b and MSA Transformer.
FALCON 1.8.8-IGB-gcc-4.9.4-Python-2.7.13 FALCON is a diploid aware genome assembler designed for Pacific Biosciences long read data.
Falcon2Fastg 0.3.1-IGB-gcc-4.9.4-Python-2.7.13 This software converts the results of PacBio assembly using FALCON, to a FASTG graph that can be visualized using Bandage.
FALCON_unzip 0.4.0-IGB-gcc-4.9.4-Python-2.7.13 FALCON-Unzip contains the modules that works with FALCON for full diploid assembly (representing haplotype specific contigs as "haplotigs" as assembly output).
fast5 0.6.2-IGB-gcc-4.9.4
0.6.3-IGB-gcc-4.9.4
0.6.5-IGB-gcc-4.9.4
0.6.5-IGB-gcc-8.2.0 		A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
fasta2 21.1.1-IGB-gcc-8.2.0
FastANI 1.32 FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes.
FastME 2.1.6.1-IGB-gcc-4.9.4
2.1.6.3-IGB-gcc-8.2.0 		FastME provides distance algorithms to infer phylogenies. FastME is based on balanced minimum evolution, which is the very principle of NJ. FastME improves over NJ by performing topological moves using fast, sophisticated algorithms.
fastmiso 0.5.4-IGB-gcc-4.9.4-Python-2.7.13 MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.
fastp 0.19.5-IGB-gcc-4.9.4
0.19.6-IGB-gcc-4.9.4-7117eba
0.20.0-IGB-gcc-4.9.4
0.23.4 		A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
fastPHASE 20160330 astPHASE is a program to estimate missing genotypes and unobserved haplotypes.
FastQ-Screen 0.14.1-IGB-gcc-8.2.0 FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect.
FastQC 0.11.5-Java-1.8.0_201
0.11.8-Java-1.8.0_152
0.11.9-Java-1.8.0_201 		FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
fastStructure 1.0-IGB-gcc-4.9.4-Python-2.7.13 fastStructure is an algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x.
FastTree 2.1.10-IGB-gcc-4.9.4
2.1.11-IGB-gcc-8.2.0 		FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
FASTX-Toolkit 0.0.14-IGB-gcc-4.9.4 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. - Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
fdupes 1.6.1-IGB-gcc-4.9.4 FDUPES is a program for identifying duplicate files residingwithin specified directories.
FEELnc 20180117-IGB-gcc-4.9.4 This document is intended to give a technical description of the FEELnc pipeline in order to annotate long non-coding RNAs (lncRNAs) based on reconstructed transcripts from RNA-seq data (either with or without a reference genome).
fermi-lite Standalone C library for assembling Illumina short reads in small regions.
FFmpeg 3.3-IGB-gcc-4.9.4
4.4-IGB-gcc-8.2.0 		A complete, cross-platform solution to record, convert and stream audio and video.
FFTW FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
fgbio 0.6.0-Java-1.8.0_152 fgbio is a command line toolkit for working with genomic and particularly next generation sequencing data.
figaro 1.1.2-IGB-gcc-8.2.0-Python-3.7.2 An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters.
file The file command is a file type guesser, that is, a command-line tool that tells you in words what kind of data a file contains.
Filtlong 0.2.1-IGB-gcc-8.2.0 Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.
fithic 2.0.7-IGB-gcc-8.2.0-Python-3.7.2 Fit-Hi-C (or FitHiC) was initially developed by Ferhat Ay, Timothy Bailey, and William Noble January 19th, 2014.
FLAC 1.3.1-IGB-gcc-4.9.4 Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.
flair 1.5-IGB-gcc-8.2.0-Python-3.7.2 FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
FLASH2 2.2.00-IGB-gcc-4.9.4 FLASH (Fast Length Adjustment of SHort reads) is an accurate and fast toolto merge paired-end reads that were generated from DNA fragments whoselengths are shorter than twice the length of reads. Merged read pairs resultin unpaired longer reads, which are generally more desired in genomeassembly and genome analysis processes.
flex Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.
flexbar 3.0.3-IGB-gcc-4.9.4 The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided.
Flye 2.4.2-IGB-gcc-4.9.4-Python-2.7.13
2.7-IGB-gcc-4.9.4-Python-3.6.1
2.7.1-IGB-gcc-8.2.0-Python-3.7.2
2.8.1-IGB-gcc-8.2.0-Python-3.7.2
2.8.2-IGB-gcc-8.2.0-Python-3.7.2
2.9-IGB-gcc-8.2.0-Python-3.7.2
2.9.2-IGB-gcc-8.2.0-Python-3.7.2 		Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
foldseek 8-ef4e960 Foldseek enables fast and sensitive comparisons of large structure sets.
foldx 5.0 The FoldX Suite builds on the strong fundament of advanced protein design features, already implemented in the successful FoldX3, and exploits the power of fragment libraries, by integrating in silico digested backbone protein fragments of different lengths. S
fontconfig Fontconfig is a library designed to provide system-wide font configuration, customization andapplication access.
fpocket 3.1.3-IGB-gcc-4.9.4 fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.
FragGeneScan 1.31-IGB-gcc-4.9.4 FragGeneScan is an application for finding (fragmented) genes in short reads.
FreeBayes 1.1.0-IGB-gcc-4.9.4
1.3.4-IGB-gcc-8.2.0 		a haplotype-based variant detector
FreeImage 3.18.0-IGB-gcc-4.9.4 FreeImage is an Open Source library project for developers who would like to support popular graphicsimage formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy touse, fast, multithreading safe.
freetype FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.
FriBidi The Free Implementation of the Unicode Bidirectional Algorithm.
fseq 1.84-Java-1.8.0_152 Tag sequencing using high-throughput sequencing technologies are now regularly employed to identify specific sequence features such as transcription factor binding sites (ChIP-seq) or regions of open chromatin (DNase-seq).
GAMS 23.6.5
32.2.0 		The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization. It consists of a language compiler and a stable of integrated high-performance solvers.
gappa 0.6.1-IGB-gcc-8.2.0 gappa is a collection of commands for working with phylogenetic data. Its main focus are evolutionary placements of short environmental sequences on a reference phylogenetic tree. Such data is typically produced by tools like EPA-ng, RAxML-EPA or pplacer and usually stored in jplace files.
GAPPadder 20170601-IGB-gcc-4.9.4 GAPPadder is designed for closing gaps on the draft genomes with paired-end reads or mate-paired reads.
gapseq 1.1-IGB-gcc-8.2.0 Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
GATK 3.7-Java-1.8.0_121
3.8-0-Java-1.8.0_121
3.8-0-Java-1.8.0_152
3.8-1-0-Java-1.8.0_152
4.0.4.0-IGB-gcc-4.9.4-Java-1.8.0_152-Python-3.6.1
4.0.9.0-IGB-gcc-4.9.4-Java-1.8.0_152-Python-3.6.1
4.1.4.0-Java-1.8.0_152
4.2.4.1-Java-1.8.0_201
4.2.6.1-Java-1.8.0_201
4.4.0.0-Java-17.0.6 		Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
Gaussian 16.C.01 Gaussian 16 is the latest in the Gaussian series of programs. It provides state-of-the-art capabilities for electronic structure modeling. Gaussian 16 is licensed for a wide variety of computer systems. All versions of Gaussian 16 contain every scientific/modeling feature, and none imposes any artificial limitations on calculations other than your computing resources and patience.
GBS-SNP-CROP 4.0-IGB-gcc-4.9.4 The GBS SNP Calling Reference Optional Pipeline (GBS-SNP-CROP) is executed via a sequence of seven Perl scripts that integrate custom parsing and filtering procedures with well-known, vetted bioinformatic tools, giving the user full access to all intermediate files.
GBSX 1.3-IGB-gcc-8.2.0-Java-1.8.0_201 Genotyping by Sequencing is an emerging technology for cost effective variant discovery and genotyping. However, current analysis tools do not fulfill all experimental design and analysis needs.
GCC The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
GCCcore The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...).
gce 1.0.2-IGB-gcc-8.2.0 GCE (genomic charactor estimator) is a bayes model based method to estimate the genome size, genomic repeat content and the heterozygsis rate of the sequencingsample
gcta 1.94.0Beta GCTA (Genome-wide Complex Trait Analysis) is a software package initially developed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for a complex trait but has been greatly extended for many other analyses of data from genome-wide association studies (GWASs).
GD 2.66-IGB-gcc-4.9.4-Perl-5.24.1
2.73-IGB-gcc-8.2.0-Perl-5.28.1 		GD.pm - Interface to Gd Graphics Library
GDAL 2.3.1-IGB-gcc-4.9.4
3.0.3-IGB-gcc-8.2.0 		GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
gdb 8.0.1-IGB-gcc-4.9.4-Python-2.7.13 The GNU Project Debugger
gdc-client 1.3.0-IGB-gcc-4.9.4-Python-2.7.13 The GDC Data Transfer Tool Client provides a command-line interface supporting both GDC data downloads and submissions.
Gdk-Pixbuf The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.
geneclass 2.0 GeneClass2 is a program employing multilocus genotypes to select or exclude populations as origins of individuals (Assignment and Migrants Detection). This is a completely rewritten new version that includes pop100gene features.
GeneMark-ES 4.33-IGB-gcc-4.9.4-Perl-5.24.1
4.33-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
4.62-IGB-gcc-8.2.0-Perl-5.28.1 		Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training.
GeneMarkS 4.30-IGB-gcc-4.9.4 GeneMarkS: a self-training method for prediction of gene starts in microbial genomes
GeneMarkS-T 5.1
gengetopt Gengetopt is a tool to write command line option parsing code for C programs. - Homepage: https://www.gnu.org/software/gengetopt/gengetopt.html
GenomeThreader 1.7.1 GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via spliced alignments. GenomeThreader was motivated by disabling limitations in GeneSeqer, a popular gene prediction program which is widely used for plant genome annotation.
genometools 1.5.10-IGB-gcc-4.9.4 The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named “libgenometools” which consists of several modules.
GenomicConsensus 2.3.3 The GenomicConsensus package provides the variantCaller tool, which allows you to apply the Quiver or Arrow algorithm to mapped PacBio reads to get consensus and variant calls.
genrich 0.6-IGB-gcc-8.2.0 Genrich is a peak-caller for genomic enrichment assays (e.g. ChIP-seq, ATAC-seq). It analyzes alignment files generated following the assay and produces a file detailing peaks of significant enrichment.
geos 3.7.1-IGB-gcc-4.9.4 GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite
GEOS GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
gettext GNU gettext is an important step for the GNU Translation Project, as it is an asset on which we maybuild many other steps. This package offers to programmers, translators, and even users, a well integrated set of toolsand documentation
gevalt 2.0-Java-1.8.0_152 GEVALT (GEnotype Visualization and ALgorithmic Tool) is designed to simplify and expedite the process of genotype analysis and disease association tests by providing a common interface to several common tasks relating to such analyses.
gfatools 0.4-IGB-gcc-4.9.4 gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED.
gff3sort 1.0.0-IGB-gcc-4.9.4-Perl-5.24.1 A Perl Script to sort gff3 files and produce suitable results for tabix tools
gffcompare 0.10.6-IGB-gcc-4.9.4 The program gffcompare can be used to compare, merge, annotate and estimate accuracy of one or more GFF files (the query files), when compared with a reference annotation (also provided as GFF).
gffread ba7535f-IGB-gcc-4.9.4 The program gffread can be used to validate, filter, convert and perform various other operations on GFF files
gffutils 0.10.1-IGB-gcc-8.2.0-Python-3.7.2
0.11.1-IGB-gcc-8.2.0-Python-3.7.2
gflags 2.2.2-IGB-gcc-4.9.4
2.2.2-IGB-gcc-8.2.0 		The gflags package contains a C++ library that implements commandline flagsprocessing. It includes built-in support for standard types such as stringand the ability to define flags in the source file in which they are used.
GFOLD 1.1.4-IGB-gcc-4.9.4 GFOLD stands for Generalized FOLD change for ranking differentially expressed genes from RNA-seq data. GFOLD is especially useful when no replicate is available. GFOLD generalizes the fold change by considering the posterior distribution of log fold change, such that each gene is assigned a reliable fold change.
GhostScript 9.21-IGB-gcc-4.9.4
9.55.0-IGB-gcc-8.2.0 		Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
git 2.28.0-IGB-gcc-8.2.0
2.9.5-IGB-gcc-4.9.4 		Git is a free and open source distributed version control system designedto handle everything from small to very large projects with speed and efficiency.
git-lfs 2.2.1-IGB-gcc-4.9.4 Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com or GitHub Enterprise.
glew 2.1.0-IGB-gcc-4.9.4 The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-sourceC/C++ extension loading library. GLEW provides efficient run-time mechanismsfor determining which OpenGL extensions are supported on the target platform.
GLib GLib is one of the base libraries of the GTK+ project
GLIMMER 3.02b-IGB-gcc-4.9.4 Glimmer is a system for finding genes in microbial DNA, especiallythe genomes of bacteria, archaea, and viruses.
GlimmerHMM 3.0.4-IGB-gcc-4.9.4 GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models.
globus-cli 3.10.1-IGB-gcc-8.2.0-Python-3.7.2
3.18.0-IGB-gcc-8.2.0-Python-3.7.2 		The CLI provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases.
glog 0.4.0-IGB-gcc-4.9.4
0.5.0-IGB-gcc-8.2.0 		A C++ implementation of the Google logging module.
glproto X protocol and ancillary headers
GMAP 2018-05-30-IGB-gcc-4.9.4
2020-06-04-IGB-gcc-8.2.0 		A Genomic Mapping and Alignment Program for mRNA and EST Sequences, andGSNAP: Genomic Short-read Nucleotide Alignment Program
GMAP-GSNAP 2017-11-15-IGB-gcc-4.9.4 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
GMP GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.
GMTK 1.4.4-IGB-gcc-4.9.4 The Graphical Models Toolkit (GMTK) is an open source, publicly available toolkit for rapidly prototyping statistical models using dynamic graphical models (DGMs) and dynamic Bayesian networks (DBNs). GMTK can be used for applications and research in speech and language processing, bioinformatics, activity recognition, and any time series application. GMTK has many features, including exact and approximate inference; a large variety of built-in factors including dense, sparse, and deterministic conditional probability tables, native support for ARPA backoff-based factors and factored language models, parameter sharing, gamma and beta distributions, dense and sparse Gaussian factors, heterogeneous mixtures, deep neural network factors, and time-inhomogeneous trellis factors; arbitrary order embedded Markov chains; a GUI-based graph viewer; flexible feature-file support and processing tools (supporting pfiles, HTK files, ASCII/binary, and HDF5 files); and both offline and streaming online inference methods that can be used for both parameter learning and prediction. More information is available in the documentation. All in all, GMTK offers a flexible, concise, and expressive probabilistic modeling framework with which one may rapidly specify a vast collection of temporal statistical models.
gnuplot 4.6.7-IGB-gcc-4.9.4
4.6.7-IGB-gcc-8.2.0
5.0.6-IGB-gcc-4.9.4 		Portable interactive, function plotting utility
GObject-Introspection GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
gofasta 0.0.3 Gofasta uses a slightly modified version of the bit-level coding scheme for nucleotides by Emmanuel Paradis (described here, and implemented in the R package ape).
gompi GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
gossamer 20170105-IGB-gcc-4.9.4 The gossamer bioinformatics suite contains goss, gossple, xenome, and electus
gperf 3.1-IGB-gcc-4.9.4
3.1-IGB-gcc-8.2.0 		GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.
Gradle 4.7 Complete Gradle install.From mobile apps to microservices, from small startups to big enterprises,Gradle helps teams build, automate and deliver better software, faster.
GraphicsMagick 1.3.26-IGB-gcc-4.9.4 GraphicsMagick is the swiss army knife of image processing.
graphlan 6ca8735-IGB-gcc-4.9.4-Python-2.7.13 GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
graphtyper 1.3-IGB-gcc-4.9.4 Graphtyper is a highly scalable genotyping software. It represents a reference genome and known variants of a genomic region using an acyclic mathematical graph structure (a "pangenome reference"), which high-throughput sequence reads are re-aligned to for the purpose of discovering and genotyping SNPs and small indels.
graphviz 2.40.1-IGB-gcc-4.9.4
2.40.1-IGB-gcc-4.9.4-Python-2.7.13 		Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
Grinder 0.5.4-IGB-gcc-4.9.4-Perl-5.24.1 Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
GROMACS 2021.2-IGB-gcc-8.2.0
2021.2-IGB-gcc-8.2.0-CUDA-11.1.0 		GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
GSL The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
gsutil 4.52-IGB-gcc-4.9.4-Python-3.6.1 gsutil is a Python application that lets you access Cloud Storage from the command line.
GTDBTk 1.5.0
2.1.1
2.3.0 		GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy GTDB
gtest 1.8.0-IGB-gcc-4.9.4 Googles C++ test framework
GTK+ 2.24.31-IGB-gcc-4.9.4-Python-2.7.13
2.24.31-IGB-gcc-4.9.4-Python-3.6.1
2.24.31-IGB-gcc-8.2.0-Python-3.7.2 		The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
gtool 0.7.5 GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
GUIDANCE 2.02-IGB-gcc-4.9.4-Perl-5.24.1 GUIDANCE is meant to be used for weighting, filtering or masking unreliably aligned positions in sequence alignments before subsequent analysis. For example, align codon sequences (nucleotide sequences that code for proteins) using PAGAN, remove columns with low GUIDANCE scores, and use the remaining alignment to infer positive selection using the branch-site dN/dS test. Other analyses where GUIDANCE filtering could be useful include phylogeny reconstruction, reconstruction of the history of specific insertion and deletion events, inference of recombination events, etc. - Homepage: http://guidance.tau.ac.il/ver2/
guideseq 20190913-IGB-gcc-8.2.0-Python-3.7.2 The guideseq package implements our data preprocessing and analysis pipeline for GUIDE-Seq data. It takes raw sequencing reads (FASTQ) and a parameter manifest file (.yaml) as input and produces a table of annotated off-target sites as output.
guppy 2.1.3
2.2.2
2.3.1
2.3.7
3.0.3
3.1.5
3.2.2
3.4.3 		Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.
guppy-gpu 2.3.1
2.3.5
2.3.7
3.0.3
3.1.5
3.2.2
3.4.3
3.5.2
3.6.0
4.0.11
4.0.15
4.2.2
4.5.3
5.0.16 		Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.
Gurobi 7.5.2 The Gurobi Optimizer was designed from the ground up to be the fastest, most powerful solver available for your LP, QP, QCP, and MIP (MILP, MIQP, and MIQCP) problems.
GUSHR 20200928-Java-1.8.0_201 Assembly-free construction of UTRs from short read RNA-Seq data on the basis of coding sequence annotation.
gzrt 0.8-IGB-gcc-8.2.0 So you thought you had your files backed up - until it came time to restore. Then you found out that you had bad sectors and you've lost almost everything because gzip craps out 10% of the way through your archive. The gzip Recovery Toolkit has a program - gzrecover - that attempts to skip over bad data in a gzip archive. This saved me from exactly the above situation. Hopefully it will help you as well.
h2o 3.14.0.3-IGB-gcc-4.9.4-R-3.3.3 R scripting functionality for H2O, the open source math engine for big data that computes parallel distributed machine learning algorithms such as generalized linear models, gradient boosting machines, random forests, and neural networks (deep learning) within various cluster environments.
h5py a toolkit for working with nanopore sequencing data from Oxford Nanopore.
hapflk 1.4-IGB-gcc-4.9.4-Python-3.6.1 hapflk is a software implementing the hapFLK and FLK tests for the detection of selection signatures based on multiple population genotyping data.
HAPO-G 1.2-IGB-gcc-8.2.0 Hapo-G (pronounced like apogee) is a tool that aims to improve the quality of genome assemblies by polishing the consensus with accurate reads.
HarfBuzz HarfBuzz is an OpenType text shaping engine.
HDF5 1.8.12-IGB-gcc-4.9.4
1.8.18-IGB-gcc-4.9.4
1.8.18-IGB-gcc-8.2.0 		HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
help2man help2man produces simple manual pages from the --help and --version output of other commands.
hhsuite 3.2.0
3.3.0-IGB-gcc-8.2.0 		The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models (HMMs).
HiC-Pro 3.1.0-IGB-gcc-8.2.0-Python-3.7.2 HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. Since version 2.7.0, HiC-Pro supports the main Hi-C protocols, including digestion protocols as well as protocols that do not require restriction enzyme such as DNase Hi-C.
HiCExplorer 2.2.1.1-IGB-gcc-8.2.0-Python-3.7.2
3.7.2-IGB-gcc-8.2.0-Python-3.7.2 		HiCExplorer addresses the common tasks of Hi-C data analysis from processing to visualization.
hifiasm 0.13-IGB-gcc-8.2.0
0.14.2-IGB-gcc-8.2.0
0.15-IGB-gcc-8.2.0
0.16.1-IGB-gcc-8.2.0
0.18.1-IGB-gcc-8.2.0
0.19.5-IGB-gcc-8.2.0
0.19.6-IGB-gcc-8.2.0
0.5-IGB-gcc-8.2.0 		Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome. Thus, it is able to keep the haplotype information as much as possible.
hifiasm-meta 0.3-IGB-gcc-8.2.0 A hifiasm fork for metagenome assembly using Hifi reads
higlass-python 0.4.4-IGB-gcc-8.2.0-Python-3.7.2 Python bindings to the HiGlass for tile serving, view config generation, and Jupyter Notebook + Lab integration.
HISAT2 2.0.5-IGB-gcc-4.9.4
2.1.0-IGB-gcc-4.9.4
2.2.0-IGB-gcc-4.9.4
2.2.1-IGB-gcc-8.2.0-Python-3.7.2 		HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
HISAT2-3N 20221013-IGB-gcc-8.2.0-Python-3.7.2 HISAT-3N (hierarchical indexing for spliced alignment of transcripts - 3 nucleotides) is designed for nucleotide conversion sequencing technologies and implemented based on HISAT2.
HMMER 2.3.2-IGB-gcc-4.9.4
2.3.2-IGB-gcc-8.2.0
3.1b2-IGB-gcc-4.9.4
3.2.1-IGB-gcc-4.9.4
3.3.1-IGB-gcc-8.2.0 		HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
HOMER 4.9.1-IGB-gcc-4.9.4-Perl-5.24.1 HOMER (Hypergeometric Optimization of Motif EnRichment) is a suite of tools for Motif Discovery and ChIP-Seq analysis. It is a collection of command line programs for unix-style operating systems written in mostly perl and c++. Homer was primarily written as a de novo motif discovery algorithm that is well suited for finding 8-12 bp motifs in large scale genomics data.
HOPS 0.33 HOPS is a java pipeline which focuses on screening MALT data for the presence of a user-specified list of target species. The pipeline essentially exists to make it easier to use MALT and MaltExtract in unison.
htop 2.2.0-IGB-gcc-4.9.4 This is htop, an interactive process viewer for Unix systems. It is a text-mode application (for console or X terminals) and requires ncurses.
HTSeq 0.12.4-IGB-gcc-8.2.0-Python-3.7.2
0.9.0-IGB-gcc-4.9.4-Python-2.7.13
0.9.1-IGB-gcc-4.9.4-Python-2.7.13 		A framework to process and analyze data from high-throughput sequencing (HTS) assays
HTSlib 1.10.2-IGB-gcc-8.2.0
1.11-IGB-gcc-8.2.0
1.12-IGB-gcc-8.2.0
1.17-IGB-gcc-8.2.0
1.4-IGB-gcc-4.9.4
1.5-IGB-gcc-4.9.4
1.9-IGB-gcc-4.9.4
1.9-IGB-gcc-8.2.0 		A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
humann 3.0.1-IGB-gcc-8.2.0-Python-3.7.2
3.1.1-IGB-gcc-8.2.0-Python-3.7.2
3.6-IGB-gcc-8.2.0-Python-3.7.2
3.7-IGB-gcc-8.2.0-Python-3.7.2 		HUMAnN (the HMP Unified Metabolic Analysis Network) is a method for efficiently and accurately profiling the abundance of microbial metabolic pathways and other molecular functions from metagenomic or metatranscriptomic sequencing data.
HUMAnN2 0.11.1-IGB-gcc-4.9.4-Python-3.6.1
0.11.2-IGB-gcc-4.9.4-Python-3.6.1 		HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
hwloc The Portable Hardware Locality (hwloc) software package provides a portable abstraction(across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, includingNUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers varioussystem attributes such as cache and memory information as well as the locality of I/O devices such asnetwork interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gatheringinformation about modern computing hardware so as to exploit it accordingly and efficiently.
hypo 1.0.3-IGB-gcc-8.2.0 HyPo--a Hybrid Polisher-- utilises short as well as long reads within a single run to polish a long reads assembly of small and large genomes. I
iced 0.5.10-IGB-gcc-8.2.0-Python-3.7.2 ICE normalization
icorn 0.97-IGB-gcc-4.9.4 Inputs: Reference Sequence (FASTA) & reads (FASTQ) & information of short reads
idba-ud 1.1.3-IGB-gcc-4.9.4 IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.
IDR 2.0.4-IGB-gcc-4.9.4-Python-3.6.1 The IDR (Irreproducible Discovery Rate) framework is a unified approach to measure the reproducibility of findings identified from replicate experiments and provide highly stable thresholds based on reproducibility. Unlike the usual scalar measures of reproducibility, the IDR approach creates a curve, which quantitatively assesses when the findings are no longer consistent across replicates. In laymans terms, the IDR method compares a pair of ranked lists of identifications (such as ChIP-seq peaks).
IGB-gcc GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
igv 2.4.4-Java-1.8.0_152
2.7.2-Java-11.0.5
2.8.0-Java-11.0.5
snapshot-Java-11.0.5 		The Integrative Genomics Viewer (IGV) is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations.
IllinoisDataBank 1.0-IGB-gcc-4.9.4-Python-3.6.1 The Illinois Data Bank is a public access repository for publishing research data from the University of Illinois at Urbana-Champaign
IM-TORNADO 2.0.3.3-IGB-gcc-4.9.4-Python-2.7.13 A pipeline for 16S reads from paired-end libraries
ImageMagick 6.9.11-58-IGB-gcc-4.9.4
7.0.5-5-IGB-gcc-4.9.4 		ImageMagick is a software suite to create, edit, compose, or convert bitmap images
impute2 2.3.2 IMPUTE2 is freely available for academic use. To see rules for non-academic use, please read the LICENCE file, which is included with each software download.
Infernal 1.1.2-IGB-gcc-4.9.4 Infernal,INFERence of RNA ALignment, is for searching DNA sequence databases for RNA structure and sequence similarities.
InterProScan 5.27-66.0-IGB-gcc-4.9.4-Java-1.8.0_152
5.28-67.0-IGB-gcc-4.9.4-Java-1.8.0_152
5.33-72.0-IGB-gcc-4.9.4-Java-1.8.0_152
5.33-72.0-IGB-gcc-4.9.4-Java-1.8.0_201
5.47-82.0-IGB-gcc-8.2.0-Java-15.0.1
5.56-89.0-IGB-gcc-8.2.0-Java-15.0.1 		InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPros signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.
intervene 0.6.5 a tool for intersection and visualization of multiple genomic region sets
ior 3.0.1-IGB-gcc-4.9.4 Parallel filesystem I/O benchmark
ipyrad 0.9.57 Welcome to ipyrad, an interactive assembly and analysis toolkit for restriction-site associated DNA (RAD-seq) and related data types. Please explore the documentation to find out more about the features of ipyrad.
IPython 5.3.0-IGB-gcc-4.9.4-Python-3.6.1 IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.
iRep 20191228-IGB-gcc-8.2.0-Python-3.7.2 iRep is a method for determining replication rates for bacteria from single time point metagenomics sequencing and draft-quality genomes.
IRFinder 1.3.1-IGB-gcc-8.2.0 Detecting intron retention from RNA-Seq experiments
isoseq3 3.7.0-0 IsoSeq v3 contains the newest tools to identify transcripts in PacBio single-molecule sequencing data. Starting in SMRT Link v6.0.0, those tools power the IsoSeq GUI-based analysis application.
ITSx 1.1.1-IGB-gcc-4.9.4 TSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
ivar 1.3.1-IGB-gcc-8.2.0 iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.
Jalview 2.11.0-Java-1.8.0_152
jansson Jansson is a C library for encoding, decoding and manipulating JSON data.
Jasmine 1.1.5 This tool is used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values.
JasPer 1.900.1-IGB-gcc-4.9.4
2.0.10-IGB-gcc-4.9.4
2.0.14-IGB-gcc-8.2.0 		The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.
Java 1.8.0_121
1.8.0_152
1.8.0_201
11.0.5
15.0.1
17.0.6 		Java Platform, Standard Edition (Java SE) lets you develop and deployJava applications on desktops and servers.
JavaFX 21 JavaFX is an open source, next generation client application platform for desktop, mobile and embedded systems built on Java.
jax-unirep 0.9-IGB-gcc-4.9.4-Python-3.6.1 Reimplementation of the UniRep protein featurization model in JAX.
Jellyfish 1.1.12-IGB-gcc-4.9.4
1.1.12-IGB-gcc-8.2.0
2.2.10-IGB-gcc-8.2.0
2.2.6-IGB-gcc-4.9.4
2.3.0-IGB-gcc-8.2.0 		Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence.
jemalloc jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
JsonCpp JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files.
Juicebox 1.11.08-Java-1.8.0_201 Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web
Juicer 1.6.0-IGB-gcc-8.2.0 Juicer is a platform for analyzing kilobase resolution Hi-C data. In this distribution, we include the pipeline for generating Hi-C maps from fastq raw data files and command line tools for feature annotation on the Hi-C maps.
juicer_tools 1.22.01-Java-1.8.0_201
JUnit A programmer-oriented testing framework for Java.
jupyter 1.0.0-IGB-gcc-4.9.4-Python-3.6.1 Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages.
jupyterlab 2.2.9-IGB-gcc-8.2.0-Python-3.7.2
3.5.0-IGB-gcc-8.2.0-Python-3.10.1 		Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages.
kallisto 0.43.1-IGB-gcc-4.9.4
0.44.0-IGB-gcc-4.9.4 		kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
KAT 2.4.1-IGB-gcc-4.9.4 KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts.
kentUtils 353-IGB-gcc-4.9.4 UCSC genome browser kent bioinformatic utilities
Keras 2.0.6-IGB-gcc-4.9.4-Python-2.7.13
2.0.8-IGB-gcc-4.9.4-Python-3.6.1
2.1.2-IGB-gcc-4.9.4-Python-3.6.1
2.1.5-IGB-gcc-4.9.4-Python-3.6.1
2.11.0-IGB-gcc-8.2.0-Python-3.7.2
2.2.0-IGB-gcc-4.9.4-Python-3.6.1
2.2.2-IGB-gcc-4.9.4-Python-3.6.1
2.2.4-IGB-gcc-4.9.4-Python-3.6.1
2.3.1-IGB-gcc-4.9.4-Python-3.6.1
2.3.1-IGB-gcc-4.9.4-Python-3.6.1-TF-2.0.3 		Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.
keras-rl 0.3.0-IGB-gcc-4.9.4-Python-2.7.13 keras-rl implements some state-of-the art deep reinforcement learning algorithms in Python and seamlessly integrates with the deep learning library Keras.
KING 2.3.2-IGB-gcc-8.2.0 KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc.
kma 1.3.24-IGB-gcc-8.2.0 KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.
KMC 3.1.1
3.2.1 		KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. The homepage of the KMC project is http://sun.aei.polsl.pl/kmc
kmerfreq 4.0-IGB-gcc-8.2.0 kmerfreq count K-mer (with size K) frequency from the input sequence data, typically sequencing reads data, and reference genome data is also applicable.
KneadData 0.10.0-IGB-gcc-8.2.0-Python-3.7.2
0.12.0-IGB-gcc-8.2.0-Python-3.7.2
0.6.1-IGB-gcc-4.9.4-Python-3.6.1
0.8.0-IGB-gcc-8.2.0-Python-3.7.2 		KneadData is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the host. However, metagenomic sequencing data from such experiments will often contain a high ratio of host to bacterial reads. This tool aims to perform principled in silico separation of bacterial reads from these contaminant reads, be they from the host, from bacterial 16S sequences, or other user-defined sources.
Kraken 1.0-IGB-gcc-4.9.4
1.1.1-IGB-gcc-8.2.0 		Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs.
Kraken2 2.0.8-beta-IGB-gcc-4.9.4
2.1.1-IGB-gcc-8.2.0
2.1.2-IGB-gcc-8.2.0 		Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs.
KrakenTools 1.2-IGB-gcc-8.2.0-Python-3.7.2 KrakenTools is a suite of scripts to be used alongside the Kraken, KrakenUniq, Kraken 2, or Bracken programs. These scripts are designed to help Kraken users with downstream analysis of Kraken results.
Krona 2.7-IGB-gcc-4.9.4-Perl-5.24.1 Interactively explore metagenomes and more from a web browser.
kyoto 20170410-IGB-gcc-4.9.4 Kyoto Tycoon is a lightweight network server on top of the Kyoto Cabinet key-value database, built for high-performance and concurrency. Some of its features include:
LAME 3.99.5-IGB-gcc-4.9.4 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
Lasagne 20170606-IGB-gcc-4.9.4-Python-2.7.13 Lasagne is a lightweight library to build and train neural networks in Theano. - Homepage: http://lasagne.readthedocs.io/en/latest/index.html
last 1257-IGB-gcc-8.2.0 LAST is designed for moderately large data (e.g. genomes, DNA reads,proteomes).
LASTZ 1.04.00-IGB-gcc-4.9.4 LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. - Homepage: http://www.bx.psu.edu/~rsharris/lastz/
lbzip2 2.5-IGB-gcc-4.9.4 lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format.
LEfSe 20180219-IGB-gcc-4.9.4-Python-2.7.13 LEfSe
Lep-MAP3 20221128-Java-15.0.1 Lep-MAP3 (LM3) is a novel linkage map construction software suite. It can handle millions of markers and thousands of individuals possibly on multiple families. Input genotype data can be from genome sequencing (RADseq or whole genome sequencing), SNP assay, microsatellites or any mixture of them.
lftp 4.9.2-IGB-gcc-8.2.0 FTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
libaec 1.0.6-IGB-gcc-8.2.0 Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers(samples). The library achieves best results for low entropy data as often encountered in space imaginginstrument data or numerical model output from weather or climate simulations. While floating point representationsare not directly supported, they can also be efficiently coded by grouping exponents and mantissa.
libBigWig A C library for reading/parsing local and remote bigWig and bigBed files. While Kent's source code is free to use for these purposes
libcerf libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.
libdap A C++ SDK which contains an implementation of DAP 2.0 and the development versions of DAP3, up to 3.4. This includes both Client- and Server-side support classes.
libdrm Direct Rendering Manager runtime library.
libevent The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.
libfaketime libfaketime intercepts various system calls that programs use to retrieve thecurrent date and time. It then reports modified (faked) dates and times (asspecified by you, the user) to these programs. This means you can modify thesystem time a program sees without having to change the time system-wide.
libffi The libffi library provides a portable, high level programming interface to various callingconventions. This allows a programmer to call any function specified by a call interface description at run-time.
libgd GD is an open source code library for the dynamic creation of images by programmers.
libgdiplus An Open Source implementation of the GDI+ API
libglvnd libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
libgpuarray 0.6.5-IGB-gcc-4.9.4 Make a common GPU ndarray(n dimensions array) that can be reused by all projects that is as future proof as possible, while keeping it easy to use for simple need/quick test. - Homepage: http://deeplearning.net/software/libgpuarray/
libgtextutils ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream - Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
libharu libHaru is a free, cross platform, open source library for generating PDF files.
libjpeg-turbo libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEGcompression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.
libpciaccess Generic PCI access library.
libpng libpng is the official PNG reference library
libpthread-stubs The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint,latency hiding, direct access to the protocol, improved threading support, and extensibility.
libreadline The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.
libsodium Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
libsvm 3.24-IGB-gcc-4.9.4 LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification.
LibTIFF tiff: Library and tools for reading and writing TIFF data files
libtool GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. - Homepage: http://www.gnu.org/software/libtool
libunwind 1.3.1-IGB-gcc-4.9.4
1.5.0-IGB-gcc-8.2.0 		The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
LibUUID Portable uuid C library
libXft X11 client-side library
libxml2 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
libxslt Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
Liftoff 1.6.1-IGB-gcc-8.2.0-Python-3.7.2 Liftoff is a tool that accurately maps annotations in GFF or GTF between assemblies of the same, or closely-related species.
lima 2.6.0-0 lima is the standard tool to identify barcode and primer sequences in PacBio single-molecule sequencing data. It powers the Demultiplex Barcodes, Iso-Seq, and Mark PCR Duplicates GUI-based analysis applications.
LINKS 1.8.5-IGB-gcc-4.9.4-Perl-5.24.1
1.8.7-IGB-gcc-4.9.4-Perl-5.24.1
1.8.7-IGB-gcc-8.2.0-Perl-5.28.1 		LINKS is a scalable genomics application for scaffolding or re-scaffolding genome assembly drafts with long reads, such as those produced by Oxford Nanopore Technologies Ltd and Pacific Biosciences. It provides a generic alignment-free framework for scaffolding and can work on any sequences. It is versatile and supports not only long sequences as a source of long-range information, but also MPET pairs and linked-reads, such as those from the 10X Genomics GemCode and Chromium platform, via ARCS (http://www.bcgsc.ca/platform/bioinfo/software/arcs). Fill gaps in LINKS-derived scaffolds using Sealer (http://www.bcgsc.ca/platform/bioinfo/software/sealer).
LittleCMS Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. - Homepage: http://www.littlecms.com/
LLVM 10.0.1-IGB-gcc-8.2.0
4.0.1-IGB-gcc-4.9.4
6.0.0-IGB-gcc-4.9.4 		The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
LMDB 0.9.22-IGB-gcc-4.9.4 LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.
lofreq 2.1.5-IGB-gcc-4.9.4-Python-2.7.13 :oFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data.
longranger 2.1.3
2.1.6
2.2.2 		Long Ranger is a set of analysis pipelines that processes Chromium sequencing output to align reads and call and phase SNPs, indels, and structural variants. There are five main pipelines, each triggered by a longranger command
lorals 20210528-IGB-gcc-8.2.0-Python-3.7.2 A Python package for allele-specific analyses in long-read data.
Loter 20210413-IGB-gcc-8.2.0-Python-3.7.2 Loter is a Python (and soon R) package for local ancestry inference [1] and haplotype phasing [2]
loupe 2.1.1 Loupe is a genome browser designed to visualize the Linked-Read data produced by the 10x Chromium Platform. Loupe is named for a jewelers loupe, which is used to inspect gems.
lpsolve 5.5.2.5-IGB-gcc-4.9.4
5.5.2.5-IGB-gcc-8.2.0 		Mixed Integer Linear Programming (MILP) solver
LRBinner 0.1-IGB-gcc-8.2.0-Python-3.7.2 Binning Error-Prone Long Reads Using Auto Encoders
LTRretriever 2.9.0-IGB-gcc-4.9.4-Perl-5.24.1 LTR_retriever is a command line program (in Perl) for accurate identification of LTR retrotransposons (LTR-RTs) from outputs of LTRharvest, LTR_FINDER, MGEScan 3.0.0, LTR_STRUC, and LtrDetector, and generates non-redundant LTR-RT library for genome annotations.
Lua 5.1.5-IGB-gcc-4.9.4
5.1.5-IGB-gcc-8.2.0
5.3.4-IGB-gcc-4.9.4 		Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
lumpy-sv 0.3.0-IGB-gcc-4.9.4 A probabilistic framework for structural variant discovery.
lz4 1.9.2-IGB-gcc-4.9.4
1.9.2-IGB-gcc-8.2.0 		LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.
lzo Portable lossless data compression library
M4 GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. - Homepage: http://www.gnu.org/software/m4/m4.html
MACS 1.4.2-1-IGB-gcc-4.9.4-Python-2.7.13 Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction.
MACS2 2.1.1.20160309-IGB-gcc-4.9.4-Python-2.7.13
2.1.2-IGB-gcc-4.9.4-Python-2.7.13
2.2.5-IGB-gcc-4.9.4-Python-3.6.1
2.2.5-IGB-gcc-8.2.0-Python-3.7.2 		Model Based Analysis for ChIP-Seq data
MAFFT 7.310-IGB-gcc-4.9.4
7.490-IGB-gcc-8.2.0 		MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.
mageck-vispr 0.5.4-IGB-gcc-4.9.4-Python-3.6.1 MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
magic 0.1-IGB-gcc-4.9.4-Python-3.6.1
0.1.1-IGB-gcc-4.9.4-Python-3.6.1 		A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data
MAKER 2.31.9-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
3.00.0-beta-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
3.01.03-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
3.01.1-beta-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded 		MAKER is a portable and easily configurable genome annotation pipeline. Its purpose is to allow smaller eukaryotic and prokaryotic genome projects to independently annotate their genomes and to create genome databases. MAKER identifies repeats, aligns ESTs and proteins to a genome, produces ab-initio gene predictions and automatically synthesizes these data into gene annotations having evidence-based quality values. MAKER is also easily trainable: outputs of preliminary runs can be used to automatically retrain its gene prediction algorithm, producing higher quality gene-models on seusequent runs. MAKERs inputs are minimal and its ouputs can be directly loaded into a GMOD database. They can also be viewed in the Apollo genome browser; this feature of MAKER provides an easy means to annotate, view and edit individual contigs and BACs without the overhead of a database. MAKER should prove especially useful for emerging model organism projects with minimal bioinformatics expertise and computer resources.
Mako 1.0.6-IGB-gcc-4.9.4-Python-3.6.1 A super-fast templating language that borrows the best ideas from the existing templating languages
manta 1.6.0-IGB-gcc-8.2.0 Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs.
mapDamage 2.0.5-IGB-gcc-4.9.4-Python-2.7.13
2.0.9-IGB-gcc-4.9.4-Python-2.7.13 		mapDamage2 is a computational framework written in Python and R, which tracks and quantifies DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms.
MAPGD 0.4.26-IGB-gcc-4.9.4 MAPGD is a series of related programs that estimate allele frequency, heterozygosity, Hardy-Weinberg disequilibrium, linkage disequilibrium and identity-by-descent (IBD) coefficients from population genomic data using a statistically rigorous maximum likelihood approach.
MapSplice 2.2.1-IGB-gcc-4.9.4-Python-2.7.13 MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.
MariaDB 10.1.31-IGB-gcc-4.9.4
10.1.31-IGB-gcc-8.2.0
10.3.17-IGB-gcc-8.2.0
5.5.58-IGB-gcc-4.9.4 		MariaDB An enhanced, drop-in replacement for MySQL.
Mash 2.2.2-IGB-gcc-8.2.0 Fast genome and metagenome distance estimation using MinHash
MashMap 2.0 MashMap implements a fast and approximate algorithm for computing local alignment boundaries between long DNA sequences. It can be useful for mapping genome assembly or long reads (PacBio/ONT) to reference genome(s).
MaskRCNN 20190227-IGB-gcc-4.9.4-Python-3.6.1 This is an implementation of Mask R-CNN on Python 3, Keras, and TensorFlow. The model generates bounding boxes and segmentation masks for each instance of an object in the image.
MaSuRCA 3.2.3-IGB-gcc-4.9.4
3.4.2-IGB-gcc-8.2.0
4.0.5-IGB-gcc-8.2.0 		MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore).
MATLAB 2017a
2017b
2020b-IGB-gcc-8.2.0 		MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran.
MATLAB-python 2017b-IGB-gcc-4.9.4-Python-3.6.1
2020b-IGB-gcc-8.2.0-Python-3.7.2 		The MATLAB Engine API for Python provides a package for Python to call MATLAB as a computational engine. The engine supports the reference implementation (CPython) for Python versions 2.7, 3.5, and 3.6.
mawk 1.3.4-20200120-IGB-gcc-8.2.0 mawk is an interpreter for the AWK Programming Language.
maxbin2 2.2.7-IGB-gcc-4.9.4 MaxBin2 is the next-generation of MaxBin (https://sourceforge.net/projects/maxbin/) that supports multiple samples at the same time.
MaxQuant 1.6.15.0-IGB-gcc-4.9.4
1.6.7.0-IGB-gcc-4.9.4 		MaxQuant is a proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.
McCortex 1.0.1-IGB-gcc-4.9.4 Multi-sample de novo assembly and variant calling using Linked de bruijn graphs. Variant calling with and without a reference genome. Between closely related samples or highly diverged ones. From bacterial to mammalian genomes. Minimal configuration. And it's free.
MCL 14.137-IGB-gcc-4.9.4
14.137-IGB-gcc-8.2.0 		The MCL algorithm is short for the Markov Cluster Algorithm, a fastand scalable unsupervised cluster algorithm for graphs (also known as networks) basedon simulation of (stochastic) flow in graphs.
MCScanX 20221031-IGB-gcc-8.2.0
medaka 0.1.0-IGB-gcc-4.9.4-Python-3.6.1 Medaka demonstrates a framework for error correcting sequencing data, particularly aimed at nanopore sequencing. Tools are provided for both training and inference. The code exploits the keras deep learning library.
MEGAHIT 1.1.1-IGB-gcc-4.9.4
1.2.9-IGB-gcc-8.2.0 		MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly.
megalodon 1.0.0-IGB-gcc-4.9.4-Python-3.6.1
2.0.0-IGB-gcc-4.9.4-Python-3.6.1
2.1.1-IGB-gcc-8.2.0-Python-3.7.2
2.2.0-IGB-gcc-8.2.0-Python-3.7.2
2.2.4-IGB-gcc-8.2.0-Python-3.7.2
2.3.4-IGB-gcc-8.2.0-Python-3.7.2 		Megalodon is a research tool for per-read and aggregated modified base and sequence variant calling by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
MEGAN 6.12.2-Java-1.8.0_152 MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.
MEME 4.11.2-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13
4.12.0-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13
5.0.1-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13
5.0.5-IGB-gcc-4.9.4
5.5.1-IGB-gcc-8.2.0 		The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
memprof 1.01 Memprof is HPC Cluster Program Profiler. It records the memory, processor, and IO usage of a process. It will then generate a graph of the results.
Meraculous-2d 2.2.6-IGB-gcc-4.9.4 Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements.
Merfin 1.1-IGB-gcc-8.2.0
20210507-IGB-gcc-8.2.0 		k-mer-based assembly and variant calling evaluation for improved consensus accuracy.
merlin-p 20181020-IGB-gcc-8.2.0 Modular regulatory network learning with per gene information (MERLIN) is a network inference method that tries to infer a more accurate regulatory network by incorporating a modularity constraint.
merqury 1.3-IGB-gcc-8.2.0 Evaluate genome assemblies with k-mers and more
meryl 1.3
Mesa 20.0.2-IGB-gcc-4.9.4 Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
Meson 0.51.2-IGB-gcc-4.9.4-Python-3.6.1 Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
MetaBAT 2.12.1
2.15-IGB-gcc-8.2.0 		MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
MetaEuk 4-IGB-gcc-8.2.0 MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to recover optimal exons sets.
MetaGeneAnnotator 20080819-x86-64 MetaGeneAnnotator is a gene-finding program for prokaryote and phage.
MetaGeneMark-2 20210406-IGB-gcc-8.2.0 MetaGeneMark-2 is an unsupervised metagenomic gene finder. It improves on MetaGeneMark by adding models for better gene start prediction, as well as automatic selection of genetic code (4 or 11).
metaMDBG 0.3 MetaMDBG is a fast and low-memory assembler for long and accurate metagenomics reads (e.g. PacBio HiFi). It is based on the minimizer de-Brujin graph (MDBG), which have been reimplemetend specifically for metagenomics assembly.
metaphlan 3.0.4-IGB-gcc-8.2.0-Python-3.7.2
3.0.7-IGB-gcc-8.2.0-Python-3.7.2
3.1.0-IGB-gcc-8.2.0-Python-3.7.2
4.0.0-IGB-gcc-8.2.0-Python-3.7.2
4.0.6-IGB-gcc-8.2.0-Python-3.7.2 		MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level.
metaphlan2 2.6.0-IGB-gcc-4.9.4-Python-3.6.1
2.7.6-IGB-gcc-4.9.4-Python-2.7.13
2.7.8-IGB-gcc-4.9.4-Python-2.7.13
2.7.8-IGB-gcc-4.9.4-Python-3.6.1 		MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
metashape 1.7.1-IGB-gcc-8.2.0
2.0.1 		Agisoft Metashape is a stand-alone software product that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales.
metashape-pro 1.8.4-IGB-gcc-8.2.0
2.0.1
2.0.2 		Agisoft Metashape is a stand-alone software product that performs photogrammetric processing of digital images and generates 3D spatial data to be used in GIS applications, cultural heritage documentation, and visual effects production as well as for indirect measurements of objects of various scales.
metashape-python 1.7.1-IGB-gcc-8.2.0-Python-3.7.2
2.0.1-IGB-gcc-8.2.0-Python-3.7.2 		Process digital images and generate 3D spatial data. Fast and highly accurate.
MetaVelvet 1.2.02-IGB-gcc-4.9.4 An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
metaviralSPAdes 20200721-IGB-gcc-8.2.0-Python-3.7.2 It contains script for viral assembly from metagenomes (assembler/metaviralspades.py), which is based on metaplasmidSPAdes.
metaWRAP 1.2.3
1.3.2 		MetaWRAP also includes a novel bin reassembly module, which allows to drastically improve the quality of a set of bins by extracting the reads belonging to each bin, and reassembling the bins with a more permissive, non-metagenomic assembler.
METIS 5.1.0-IGB-gcc-4.9.4 METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes,and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on themultilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes.
mfold 4.7-IGB-gcc-8.2.0 The mfold web server is one of the oldest web servers in computational molecular biology.
microbiomeutil 20110519-IGB-gcc-4.9.4 Contains ChimeraSlayer, WigeoN, and NAST-iEr
microbiome_helper 20171114-IGB-gcc-4.9.4 An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools. We provide workflows, tutorials and a virtual box image to help researchers process microbial data.
miniasm 0.2-IGB-gcc-4.9.4 Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream assemblers, miniasm does not have a consensus step. It simply concatenates pieces of read sequences to generate the final unitig sequences. Thus the per-base error rate is similar to the raw input reads.
Miniconda2 4.7.12.1 Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
Miniconda3 23.5.2
4.10.3
4.7.12.1 		Built to complement the rich, open source Python community,the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.
minimap 0.2-IGB-gcc-4.9.4
2.11-IGB-gcc-4.9.4
2.16-IGB-gcc-4.9.4-Python-3.6.1
2.17-IGB-gcc-8.2.0
2.18-IGB-gcc-8.2.0
2.21-IGB-gcc-8.2.0
2.3-IGB-gcc-4.9.4
2.8-IGB-gcc-4.9.4 		Minimap is an experimental tool to efficiently find multiple approximate mapping positions between two sets of long sequences, such as between reads and reference genomes, between genomes and between long noisy reads.
minorseq 20180314-IGB-gcc-4.9.4 Minor Variant Calling and Phasing Tools
mirdeep2 0.0.8-IGB-gcc-4.9.4
0.1.3-IGB-gcc-4.9.4 		miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
mitofates 1.2-IGB-gcc-4.9.4-Perl-5.24.1 MitoFates predicts mitochondrial presequence, a cleavable localization signal located in N-terminal, and its cleaved position.
mlst 2.19.0-IGB-gcc-8.2.0-Perl-5.28.1 Scan contig files against traditional PubMLST typing schemes
mmquant 1.0.4-IGB-gcc-8.2.0 A tool to quantiy gene expression. The mmquant algorithm handles multiply mapping reads, i.e., duplicated genes by constructing merged genes.
MMseqs2 10-6d92c MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.
modeltest-ng 0.1.7 ModelTest-NG is a tool for selecting the best-fit model of evolution for DNA and protein alignments. ModelTest-NG supersedes jModelTest and ProtTest in one single tool, with graphical and command console interfaces.
Mono An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
MOODS 1.9.4.1-IGB-gcc-8.2.0-Python-3.7.2 MOODS is a suite of algorithms for matching position weight matrices (PWM) against DNA sequences. It features advanced matrix matching algorithms implemented in C++ that can be used to scan hundreds of matrices against chromosome-sized sequences in few seconds.
Mothur 1.38.1.1
1.39.5
1.39.5-IGB-gcc-4.9.4
1.44.1-IGB-gcc-8.2.0
1.47.0-IGB-gcc-8.2.0 		Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
MPFR The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.
MPICH 3.0.4-GCC-4.9.4-2.28 MPICH v3.x is an open source high-performance MPI 3.0 implementation.It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
msgpack It's like JSON but smaller and faster.
msmc 1.1.0 This software implements MSMC, a method to infer population size and gene flow from multiple genome sequences
mspminer 2.0 MSPminer reconstitutes Metagenomic Species Pan-genomes by binning co-abundant genes across metagenomic samples.
MToolBox 1.0-IGB-gcc-4.9.4
1.2.1-IGB-gcc-4.9.4 		MToolBox is a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. MToolBox includes an updated computational strategy to assemble mitochondrial genomes from Whole Exome and/or Genome Sequencing (PMID: 22669646) and an improved fragment-classify tool (PMID:22139932) for haplogroup assignment, functional and prioritization analysis of mitochondrial variants. MToolBox provides pathogenicity scores, profiles of genome variability and disease-associations for mitochondrial variants. MToolBox provides also a Variant Call Format file (version 4.0) featuring, for the first time, allele-specific heteroplasmy.
multigeneblast 1.1.12-IGB-gcc-4.9.4 MultiGeneBlast is an open source tool for identification of homologs of multigene modules such as operons and gene clusters. It is based on a reformatting of the FASTA headers of NCBI GenBank protein entries, using which it can track down their source nucleotide and coordinates.
MultiQC 0.9-IGB-gcc-4.9.4-Python-2.7.13
1.11-IGB-gcc-8.2.0-Python-3.7.2
1.14-IGB-gcc-8.2.0-Python-3.7.2
1.15-IGB-gcc-8.2.0-Python-3.7.2
1.2-IGB-gcc-4.9.4-Python-2.7.13
1.6-IGB-gcc-4.9.4-Python-3.6.1
1.7-IGB-gcc-4.9.4-Python-3.6.1
1.7-IGB-gcc-8.2.0-Python-3.7.2
1.9-IGB-gcc-8.2.0-Python-3.7.2 		MultiQC searches a given directory for analysis logs and compiles a HTML report. Its a general use tool, perfect for summarising the output from numerous bioinformatics tools.
MUMmer 3.23-IGB-gcc-4.9.4
3.23-IGB-gcc-8.2.0
4.0.0beta2-IGB-gcc-4.9.4
4.0.0beta2-IGB-gcc-8.2.0
4.0.0rc1-IGB-gcc-8.2.0 		MUMmer is a system for rapidly aligning entire genomes
MUSCLE 3.8.31-IGB-gcc-4.9.4 MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks. - Homepage: http://drive5.com/muscle/
NAMD 20200428 is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems.
nanopack 1.0.0-IGB-gcc-4.9.4-Python-3.6.1 Easily install all my long read processing and analysis scripts simultaneously.
NanoPlot 1.18.2-IGB-gcc-4.9.4-Python-3.6.1 Plotting tool for long read sequencing data and alignments.
nanopolish 0.10.1-IGB-gcc-4.9.4
0.10.2-IGB-gcc-4.9.4
0.11.0-IGB-gcc-4.9.4
0.13.2-IGB-gcc-8.2.0
0.6.0-IGB-gcc-4.9.4
0.7.1-IGB-gcc-4.9.4
0.7.1-IGB-gcc-4.9.4-159d92b
0.8.3-IGB-gcc-4.9.4
0.8.5-IGB-gcc-4.9.4
0.9.0-IGB-gcc-4.9.4 		Software package for signal-level analysis of Oxford Nanopore sequencing data.
NanoSV 1.2.4-IGB-gcc-8.2.0-Python-3.7.2 NanoSV is a software package that can be used to identify structural genomic variations in long-read sequencing data, such as data produced by Oxford Nanopore Technologies’ MinION, GridION or PromethION instruments, or Pacific Biosciences RSII or Sequel sequencers.
NASM NASM: General-purpose x86 assembler
ncbi-datasets 20220607
20221101
20240305 		Install and use the NCBI Datasets command line tools
ncbi-genome-download 0.2.9-IGB-gcc-4.9.4-Python-3.6.1 Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago.
ncbi-toolkit 22-IGB-gcc-8.2.0 The NCBI Toolkit is a collection of utilities developed for the production and distribution of GenBank, Entrez, BLAST, and related services by the National Center for Biotechnology Information.
ncbi-vdb 2.11.0-IGB-gcc-8.2.0
2.8.2-IGB-gcc-4.9.4 		The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
ncdf4 1.16-IGB-gcc-4.9.4-R-3.3.3 This package provides a high-level R interface to data files written using Unidatas netCDF library (version 4 or earlier), which are binary data files that are portable across platforms and include metadata information in addition to the data sets.
NCO 4.7.2-IGB-gcc-4.9.4
5.0.1-IGB-gcc-8.2.0 		manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5
ncurses The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
ncview 2.1.7-IGB-gcc-8.2.0 Ncview is a visual browser for netCDF format files.Typically you would use ncview to get a quick and easy, push-buttonlook at your netCDF files. You can view simple movies of the data,view along various dimensions, take a look at the actual data values,change color maps, invert the data, etc.
netCDF 4.4.1.1-IGB-gcc-4.9.4
4.7.2-IGB-gcc-8.2.0 		NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
netCDF-Fortran 4.4.1-IGB-gcc-4.9.4
4.5.2-IGB-gcc-8.2.0 		NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
NetLogo 5.2.1
6.0.3 		NetLogo is a multi-agent programmable modeling environment. It is used by many tens of thousands of students, teachers and researchers worldwide.
nettle 3.3-IGB-gcc-4.9.4 Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space.
nextflow 0.25.7-Java-1.8.0_121
0.26.3-Java-1.8.0_152
18.10.1-Java-1.8.0_152
19.07.0-Java-1.8.0_152
20.01.0-Java-1.8.0_152
21.03.0-Java-1.8.0_152
21.03.0-Java-1.8.0_201
21.04.1-Java-1.8.0_152
21.06.0-edge-Java-1.8.0_152
22.09.7-Java-11.0.5
22.10.1-Java-15.0.1
22.10.6-Java-15.0.1
23.10.0-Java-15.0.1 		Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
NextPolish 1.4.0-IGB-gcc-8.2.0 NextPolish is used to fix base errors (SNV/Indel) in the genome generated by noisy long reads, it can be used with short read data only or long read data only or a combination of both.
nf-core 1.6-IGB-gcc-4.9.4-Python-3.6.1
2.7.2-IGB-gcc-8.2.0-Python-3.10.1 		A community effort to collect a curated set of analysis pipelines built using Nextflow.
NGS NGS is a new, domain-specific API for accessing reads, alignments and pileupsproduced from Next Generation Sequencing.
NGSCheckMate 20190507-IGB-gcc-8.2.0-Python-2.7.18 NGSCheckMate is a software package for identifying next generation sequencing (NGS) data files from the same individual. It analyzes various types of NGS data files including (but not limited to) whole genome sequencing (WGS), whole exome sequencing (WES), RNA-seq, ChIP-seq, and targeted sequencing of various depths.
ngsF 1.2.0-IGB-gcc-8.2.0 ngsF is a program to estimate per-individual inbreeding coefficients under a probabilistic framework that takes the uncertainty of genotype's assignation into account. It avoids calling genotypes by using genotype likelihoods or posterior probabilities.
ngsF-HMM 20200722-IGB-gcc-8.2.0 ngsF-HMM is a program to estimate per-individual inbreeding tracts using a two-state Hidden Markov Model (HMM).
ngsLD 1.2.0-IGB-gcc-8.2.0 ngsLD is a program to estimate pairwise linkage disequilibrium (LD) taking the uncertainty of genotype's assignation into account. It does so by avoiding genotype calling and using genotype likelihoods or posterior probabilities.
ninja 1.8.2-IGB-gcc-4.9.4 Ninja is a small build system with a focus on speed. It differs from other build systems in two major respects: it is designed to have its input files generated by a higher-level build system, and it is designed to run builds as fast as possible.
NINJA 0.97-IGB-gcc-4.9.4 Nearly Infinite Neighbor Joining Application
Ninja 1.9.0-IGB-gcc-4.9.4 Ninja is a small build system with a focus on speed.
nltk 3.5-IGB-gcc-4.9.4-Python-3.6.1
3.5-IGB-gcc-8.2.0-Python-3.7.2 		NLTK -- the Natural Language Toolkit -- is a suite of open source Python modules, data sets, and tutorials supporting research and development in Natural Language Processing.
nodejs 10.16.2-IGB-gcc-4.9.4
14.15.0-IGB-gcc-8.2.0
9.9.0-IGB-gcc-4.9.4 		Node.js is a platform built on Chromes JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
nonpareil 3.3.4-IGB-gcc-8.2.0 Estimate average coverage and create Nonpareil curves for metagenomic datasets.
nose-parameterized 0.6.0-IGB-gcc-4.9.4-Python-2.7.13 Parameterized testing with any Python test framework.
novocraft 3.08.00 Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms.
npm v7.20.0-IGB-gcc-4.9.4 the package manager for JavaScript
NucleoATAC 0.3.4-IGB-gcc-4.9.4-Python-2.7.13 NucleoATAC is a python package for calling nucleosome positions and occupancy using ATAC-Seq data. Functions for calling nucleosomes are included in the nucleoatac command-line function. NucleoATAC also includes other utlities for working with ATAC-seq data under the pyatac function.
numactl The numactl program allows you to run your application program on specific cpus and memory nodes.It does this by supplying a NUMA memory policy to the operating system before running your program.The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.
numba 0.34.0-IGB-gcc-4.9.4-Python-2.7.13
0.34.0-IGB-gcc-4.9.4-Python-3.6.1
0.35.0-IGB-gcc-4.9.4-Python-2.7.13
0.52.0-IGB-gcc-8.2.0-Python-3.7.2
0.55.2-IGB-gcc-8.2.0-Python-3.7.2
0.59.0-IGB-gcc-8.2.0-Python-3.10.1 		Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.
numpy The fundamental package for scientific computing with Python
NWChem 6.6.revision27746-IGB-gcc-4.9.4-Python-2.7.13 NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity.
OBITools3 3.0.0b42-IGB-gcc-8.2.0-Python-3.7.2 The OBITools3: A package for the management of analyses and data in DNA metabarcoding
OCaml 4.05.0-IGB-gcc-4.9.4 OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming.
octopus 0.6.3-beta-IGB-gcc-8.2.0 Octopus is a mapping-based variant caller that implements several calling models within a unified haplotype-aware framework. Octopus takes inspiration from particle filtering by constructing a tree of haplotypes and dynamically pruning and extending the tree based on haplotype posterior probabilities in a sequential manner.
OligoMiner 20181123-IGB-gcc-4.9.4 A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
Omni-C 20210526-IGB-gcc-8.2.0-Python-3.7.2 The Dovetail™ Omni-C™ library uses a sequence-independent endonuclease for chromatin digestion prior to proximity ligation and library generation.
ont-fast5-api 3.1.5-IGB-gcc-8.2.0-Python-3.7.2
3.3.0-IGB-gcc-8.2.0-Python-3.7.2 		ont_fast5_api is a simple interface to HDF5 files of the Oxford Nanopore .fast5 file format.
OpenBabel 3.0.0-IGB-gcc-8.2.0 Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
OpenBLAS OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
OpenCV 3.1.0-IGB-gcc-4.9.4-Python-2.7.13
3.3.0-IGB-gcc-4.9.4-Python-3.6.1
4.5.2-IGB-gcc-8.2.0-Python-3.7.2 		OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products.
OpenMPI 2.1.0-GCC-4.9.4-2.28
4.0.0-GCC-8.2.0-2.32 		The Open MPI Project is an open source MPI-3 implementation.
OpenPGM OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.
OpenSfM 0.5.1-IGB-gcc-8.2.0-Python-3.7.2 OpenSfM is a Structure from Motion library written in Python. The library serves as a processing pipeline for reconstructing camera poses and 3D scenes from multiple images.
OpenSSL 1.1.1m-IGB-gcc-8.2.0 The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library.
OrthoFinder 2.2.7
2.3.7-IGB-gcc-4.9.4
2.5.4-IGB-gcc-8.2.0 		OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics. It finds orthologs and orthogroups, infers rooted gene trees for all orthogroups and identifies all of the gene duplcation events in those gene trees.
OrthoMCL 2.0.9-IGB-gcc-4.9.4-Perl-5.24.1 OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. - Homepage: http://orthomcl.org/
OutPredict 1.0.0-IGB-gcc-8.2.0-Python-3.7.2 This repository contains OutPredict, a python developed Method for Predicting Out-of-sample Data in Time Series and Steady State data as well as to predict Causal connections from transcription factors to genes.
p7zip 17.04-IGB-gcc-8.2.0 p7zip is a quick port of 7z.exe and 7za.exe (CLI version of7zip) for Unix. 7-Zip is a file archiver with highest compression ratio.
Pacasus 1.2-IGB-gcc-4.9.4-Python-2.7.13 Tool for detecting and cleaning PacBio / Nanopore long reads after whole genome amplification.
PAGAN 20150723-IGB-gcc-4.9.4 PAGAN is a general-purpose method for the alignment of sequence graphs. PAGAN is based on the phylogeny-aware progressive alignment algorithm and uses graphs to describe the uncertainty in the presence of characters at certain sequence positions. However, graphs also allow describing the uncertainty in input sequences and modelling e.g. homopolymer errors in Roche 454 reads, or representing inferred ancestral sequences against which other sequences can then be aligned. PAGAN is still under development and will hopefully evolve to an easy-to-use, general-purpose method for phylogenetic sequence alignment.
pagit 1.0 Tools to generate automatically high quality sequence by ordering contigs, closing gaps, correcting sequence errors and transferring annotation.
pairix 0.3.7-IGB-gcc-8.2.0 Pairix is a tool for indexing and querying on a block-compressed text file containing pairs of genomic coordinates.
pairtools 0.3.0-IGB-gcc-4.9.4-Python-3.6.1
1.0.2-IGB-gcc-8.2.0-Python-3.7.2 		pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment.
pal2nal 14-IGB-gcc-4.9.4 PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment.
PAML 4.9e-IGB-gcc-4.9.4 PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. - Homepage: http://abacus.gene.ucl.ac.uk/software/paml.html
PANDAseq 2.11-IGB-gcc-4.9.4 PANDAseq assembles Illumina Solexa overlapping pair-end reads. - Homepage: https://github.com/neufeld/pandaseq
pandoc 2.2.3.2 If you need to convert files from one markup format into another, pandoc is your swiss-army knife
Pango Pango is a library for laying out and rendering of text, with an emphasis on internationalization.Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in thecontext of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
pangolin 2.3.2-IGB-gcc-8.2.0-Python-3.7.2
2.4.2-IGB-gcc-8.2.0-Python-3.7.2 		Phylogenetic Assignment of Named Global Outbreak LINeages
parabricks 3.1.0-IGB-gcc-8.2.0-Python-3.7.2
3.7.0 		NVIDIA Clara™ Parabricks is a computational framework supporting genomics applications from DNA to RNA. It employs NVIDIA’s CUDA, HPC, AI, and data analytics stacks to build GPU accelerated libraries, pipelines, and reference application workflows for primary, secondary, and tertiary analysis.
parallel 20170622-IGB-gcc-4.9.4
20200822-IGB-gcc-8.2.0 		parallel: GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
pb-assembly 0.0.6
0.0.8 		PacBio Assembly Tool Suite
pbaa 1.0.3.0 PacBio Amplicon Analysis (pbaa) separates complex mixtures of amplicon targets from genomic samples. The pbaa application is designed to cluster and generate high-quality consensus sequences from HiFi reads.
pbbam 1.0.7-IGB-gcc-8.2.0 The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. These components include a core C++ library, bindings for additional languages, and command-line utilities.
pbccs 4.0
6.4.0 		ccs takes multiple subreads of the same SMRTbell molecule and combines them using a statistical model to produce one highly accurate consensus sequence, also called HiFi read, with base quality values.
pbipa 1.3.0
1.3.2 		Improved Phased Assembler (IPA) is the official PacBio software for HiFi genome assembly. IPA was designed to utilize the accuracy of PacBio HiFi reads to produce high-quality phased genome assemblies.
pbmm2 1.12.0
1.4.0 		pbmm2 is a SMRT C++ wrapper for minimap2's C API. Its purpose is to support native PacBio in- and output, provide sets of recommended parameters, generate sorted output on-the-fly, and postprocess alignments.
pbzip2 1.1.13-IGB-gcc-4.9.4
1.1.13-IGB-gcc-8.2.0 		PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines.
pcangsd 0.9-IGB-gcc-4.9.4-Python-2.7.13
20220330-IGB-gcc-8.2.0-Python-3.7.2 		Framework for analyzing low-depth next-generation sequencing (NGS) data in heterogeneous/structured populations using principal component analysis (PCA).
PCRE The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PCRE2 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
PEAKachu 0.1.0-IGB-gcc-8.2.0-Python-3.7.2 Peak calling tool for CLIP-seq data
PEAR 0.9.8-IGB-gcc-4.9.4 PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. - Homepage: http://sco.h-its.org/exelixis/web/software/pear/
PEnG-motif 1.0.1 PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.
PePr 1.1.21-IGB-gcc-4.9.4-Python-2.7.13 PePr is a ChIP-Seq Peak-calling and Prioritization pipeline that uses a sliding window approach and models read counts across replicates and between groups with a negative binomial distribution.
Peregrine 1.5.4 Peregrine & SHIMMER Genome Assembly Toolkit
perfsuite 1.1.4-IGB-gcc-4.9.4 PerfSuite is a collection of tools, utilities, and libraries for software performance analysis where the primary design goals are ease of use, comprehensibility, interoperability, and simplicity. This software can provide a good "entry point" for more detailed performance analysis and can help point the way towards selecting other tools and/or techniques using more specialized software if necessary (for example, tools/libraries from academic research groups or third-party commercial software).
Perl 5.24.1-IGB-gcc-4.9.4
5.24.1-IGB-gcc-4.9.4-bare
5.26.1-IGB-gcc-4.9.4-unthreaded
5.28.1-IGB-gcc-8.2.0 		Larry Wall's Practical Extraction and Report Language
pfamscan 1.6-IGB-gcc-4.9.4-Perl-5.24.1 This readme should help you get started with "pfam_scan.pl", which is for usewith the HMMER3 version of HMMER.
pfilt 1.5-IGB-gcc-8.2.0 The pfilt program is designed to mask out (i.e. replace amino acid characterswith Xs) regions of low complexity, coiled-coil regions and more regions withextremely biased amino acid compositions.
pftoolsV3 3.2.12-IGB-gcc-8.2.0 A suite of tools to build and search generalized profiles (protein and DNA).
PGDSpider 2.1.1.5-Java-1.8.0_201 PGDSpider is a powerful automated data conversion tool for population genetic and genomics programs. It facilitates the data exchange possibilities between programs for a vast range of data types (e.g. DNA, RNA, NGS, microsatellite, SNP, RFLP, AFLP, multi-allelic data, allele frequency or genetic distances).
pgmpy 20180320-IGB-gcc-4.9.4-Python-3.6.1 pgmpy is a python library for working with Probabilistic Graphical Models.
Phantompeaktools 1.2-IGB-gcc-4.9.4-R-3.4.1 Custom SPP for Phantompeaktools
Phantompeaktools-spp Custom SPP for Phantompeaktools
PhiSpy 2.3-IGB-gcc-4.9.4-Python-2.7.13 A novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies
phobius 1.01 A combined transmembrane topology and signal peptide predictor
phrap 1.090518-IGB-gcc-8.2.0 A Finishing Package (BAM File Viewer, Assembly Editor, Autofinish, Autoreport, Autoedit, and Align Reads To Reference Sequence)
phyloFlash 3.3-IGB-gcc-4.9.4 phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset.
phylophlan 3.0.1-IGB-gcc-8.2.0-Python-3.7.2
3.0.3-IGB-gcc-8.2.0-Python-3.7.2 		PhyloPhlAn 3.0 is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
phylophlan2 0.34-IGB-gcc-4.9.4-Python-3.6.1 PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
PhyloSift 1.0.0_01-IGB-gcc-4.9.4-Perl-5.24.1 PhyloSift is a suite of software tools to conduct phylogeneticanalysis of genomes and metagenomes.
picard 1.77-Java-1.8.0_152
2.10.1-Java-1.8.0_152
2.27.5-Java-1.8.0_201
2.9.0-Java-1.8.0_121
2.9.4-Java-1.8.0_121 		A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.
PICRUSt 1.1.1-IGB-gcc-4.9.4-Python-2.7.13
1.1.3-IGB-gcc-4.9.4-Python-2.7.13 		PICRUSt (pronounced pie crust) is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.
PICRUSt2 2.3.0-b-IGB-gcc-8.2.0-Python-3.7.2
2.4.1-IGB-gcc-8.2.0-Python-3.7.2 		PICRUSt2 (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) is a software for predicting functional abundances based only on marker gene sequences.
pigz 2.3.4-IGB-gcc-4.9.4
2.4-IGB-gcc-8.2.0 		pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.
Pillow 5.1.0-IGB-gcc-4.9.4-Python-2.7.13
5.1.0-IGB-gcc-4.9.4-Python-3.6.1 		Pillow is the friendly PIL fork by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
pilon 1.22-Java-1.8.0_121
1.23-Java-1.8.0_152 		Pilon is a software tool which can be used to:- Automatically improve draft assemblies- Find variation among strains, including large event detection
piranha 1.2.1-IGB-gcc-4.9.4 iranha is a peak-caller for CLIP- and RIP-Seq data. It takes input in BED or BAM format and identifies regions of statistically significant read enrichment. Additional covariates may optionally be provided to further inform the peak-calling process.
PITA 6-IGB-gcc-4.9.4 The PITA executable allows you to identify and score microRNA targets on UTRs.
pixman Pixman is a low-level software library for pixel manipulation, providing features such as imagecompositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.
pkg-config pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries).
plass 2-c7e35-IGB-gcc-4.9.4
3-764a3 		Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.
plastid 0.5.1-IGB-gcc-8.2.0-Python-3.7.2 plastid is a Python library for genomics and sequencing. It includes tools for exploratory data analysis (EDA) as well as a handful of scripts that implement common tasks.
platanus 1.2.4 Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences ofhighly heterozygous diploids from massively parallel shotgun sequencing data.
Platypus 20180622-IGB-gcc-4.9.4-Python-2.7.13 The Platypus variant caller.
plink 1.07
1.90 		This is a comprehensive update to Shaun Purcells PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDKs Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others.
plotsr 1.1.1-IGB-gcc-8.2.0-Python-3.10.1 Plotsr generates high-quality visualisation of synteny and structural rearrangements between multiple genomes. For this, it uses the genomic structural annotations between multiple chromosome-level assemblies.
pomoxis 0.1.0-IGB-gcc-4.9.4-Python-3.6.1 Pomoxis contains a set of services to perform analysis of squiggles as they are produced in real-time along with fast pipelines for generating draft assemblies.
popins 1.0.1-IGB-gcc-8.2.0 Population-scale detection of novel-sequence insertions.
popins2 20220127-IGB-gcc-8.2.0 Population-scale detection of non-reference sequence variants using colored de Bruijn Graphs
popoolation2 1201-IGB-gcc-8.2.0-Perl-5.28.1 PoPoolation2 allows to compare allele frequencies for SNPs between two or more populations and to identify significant differences.
poppler Poppler is a PDF rendering library based on the xpdf-3.0 code base.
popscle 20210504-IGB-gcc-8.2.0 popscle is a suite of population scale analysis tools for single-cell genomics data. The key software tools in this repository includes demuxlet (version 2) and freemuxlet, a genotyping-free method to deconvolute barcoded cells by their identities while detecting doublets.
Porechop 0.2.3-IGB-gcc-4.9.4-Python-3.6.1 Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.
poretools 0.6.0-IGB-gcc-4.9.4-Python-2.7.13 a toolkit for working with nanopore sequencing data from Oxford Nanopore.
ppanini 0.7.3.1-IGB-gcc-4.9.4-Python-2.7.13 PPANINI (Prioritization and Prediction of functional Annotation for Novel and Important genes via automated data Network Integration) is a computational pipeline that ranks genes by employing a combination of community parameters such as prevalence and abundance across samples.
pplacer 1.1.alpha19
1.1.alpha19-IGB-gcc-8.2.0-Python-3.7.2 		Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis.
PRANK 170427-IGB-gcc-4.9.4 PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. It’s based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. In addition, PRANK borrows ideas from maximum likelihood methods used in phylogenetics and correctly takes into account the evolutionary distances between sequences. Lastly, PRANK allows for defining a potential structure for sequences to be aligned and then, simultaneously with the alignment, predicts the locations of structural units in the sequences.
preseq 2.0.3-IGB-gcc-4.9.4
3.1.2-IGB-gcc-8.2.0 		The preseq package is aimed at predicting and estimating the complexity of a genomic sequencing library, equivalent to predicting and estimating the number of redundant reads from a given sequencing depth and how many will be expected from additional sequencing using an initial sequencing experiment.
primer3 2.4.0-IGB-gcc-4.9.4 Primer3 is a widely used program for designing PCR primers (PCR = "Polymerase Chain Reaction"). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers.
prinseq 0.20.4-IGB-gcc-4.9.4-Perl-5.24.1 PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data.
Prodigal 2.6.3 Fast, reliable protein-coding gene prediction for prokaryotic genomes.
PROJ Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
prokka 1.13-IGB-gcc-4.9.4-Perl-5.24.1
1.14.6-IGB-gcc-4.9.4-Perl-5.24.1
1.14.6-IGB-gcc-8.2.0-Perl-5.28.1 		Whole genome annotation is the process of identifying features of interest in a set of genomic DNA sequences, and labelling them with useful information. Prokka is a software tool to annotate bacterial, archaeal and viral genomes quickly and produce standards-compliant output files.
Prost 0.7.45-IGB-gcc-4.9.4-Python-2.7.13 Prost (PRocessing Of Small Transcripts) is a python application that quantifies and annotates microRNA (miRNA) expression in metazoans with assembled genomes. Prost works by counting short transcripts within a user-specifiable length range. These counted transcripts are aligned to a user specifiable genome allowing for post-transcriptional modification (e.g. untemplated additions, editing, alternative cutting) and then "binned" together based on genomic location. Each bin is then annotated with databases of mature miRNAs, hairpins, and other types of RNAs (the databases may be derived from miRBase, Ensembls BioMart, other databases, or may be custom built by the user).
proteinfer 20220411-IGB-gcc-4.9.4-Python-3.6.1 ProteInfer is an approach for predicting the functional properties of protein sequences using deep neural networks.
ProtHint 2.5.0-IGB-gcc-8.2.0
2.6.0-IGB-gcc-8.2.0 		ProtHint is a pipeline for predicting and scoring hints (in the form of introns, start and stop codons) in the genome of interest by mapping and spliced aligning predicted genes to a database of reference protein sequences.
protobuf 2.6.1-IGB-gcc-4.9.4
23.4-IGB-gcc-8.2.0
3.5.0-IGB-gcc-4.9.4 		Protocol Buffers (a.k.a., protobuf) are Googles language-neutral, platform-neutral, extensible mechanism for serializing structured data.
protobuf-python 3.19.4-IGB-gcc-8.2.0 Python Protocol Buffers runtime library.
prottest3 3.4.2 ProtTest is a bioinformatic tool for the selection of best-fit models of aminoacid replacement for the data at hand. ProtTest makes this selection by finding the model in the candidate list with the smallest Akaike Information Criterion (AIC), Bayesian Information Criterion (BIC) score or Decision Theory Criterion (DT).
psipred 4.0-IGB-gcc-8.2.0
4.02-IGB-gcc-8.2.0 		The PSIPRED Workbench provides a range of protein structure prediction methods. The site can be used interactively via a web browser or programmatically via our REST API. For high-throughput analyses, downloads of all the algorithms are available.
pssh 2.3.1-IGB-gcc-4.9.4-Python-2.7.13 PSSH provides parallel versions of OpenSSH and related tools, including pssh, pscp, prsync, pnuke and pslurp. This project includes psshlib which can be used within custom applications.
pullseq 1.0.2-IGB-gcc-4.9.4 Utility program for extracting sequences from a fasta/fastq file
purge_dups 1.0.1-IGB-gcc-8.2.0-Python-3.7.2
1.2.5-IGB-gcc-8.2.0-Python-3.7.2 		purge haplotigs and overlaps in an assembly based on read depth
purge_haplotigs 1.1.1-IGB-gcc-8.2.0 A simple pipeline for reassigning primary contigs that should be labelled as haplotigs.
py2cytoscape 0.7.1-IGB-gcc-8.2.0-Python-3.7.2 py2cytoscape is a collection of utilities to use Cytoscape and Cytoscape.js from Python. Network visualization feature is still limited in Python, but with this tool, you can access both of Cytoscape and Cytoscape.js as network visualization engines for your Python code!
pyani 0.2.10-IGB-gcc-4.9.4-Python-3.6.1 Python module for average nucleotide identity analyses
pybedtools 0.7.10-IGB-gcc-4.9.4-Python-3.6.1
0.8.2-IGB-gcc-8.2.0-Python-3.7.2
0.9.0-IGB-gcc-8.2.0-Python-3.7.2 		pybedtools is a Python package that wraps BEDTools, so you will need both installed.
pybind11 2.9.2-IGB-gcc-8.2.0 pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.
pycairo 1.19.1-IGB-gcc-8.2.0-Python-3.7.2 Pycairo is a Python module providing bindings for the cairo graphics library. It depends on cairo >= 1.15.10 and works with Python 3.7+. Pycairo, including this documentation, is licensed under the LGPL-2.1-only OR MPL-1.1.
PyCUDA 2017.1-IGB-gcc-4.9.4-Python-2.7.13 PyCUDA lets you access Nvidia‘s CUDA parallel computation API from Python. - Homepage: https://mathema.tician.de/software/pycuda/
pyCUDA 2024.1-IGB-gcc-8.2.0-Python-3.10.1 PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python. Several wrappers of the CUDA API already exist-so what’s so special about PyCUDA?
pyfasta 0.5.2-IGB-gcc-4.9.4-Python-2.7.13 Stores a flattened version of the fasta file without spaces or headers and uses either a mmap of numpy binary format or fseek/fread so the sequence data is never read into memory.
pyGenomeTracks 3.8-IGB-gcc-8.2.0-Python-3.7.2 pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable.
pygpu 0.6.5-IGB-gcc-4.9.4-Python-2.7.13 Python bindings for libgpuarray - Homepage: http://deeplearning.net/software/libgpuarray
pygraphviz 1.3.1-IGB-gcc-4.9.4-Python-3.6.1 PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms.
pylearn2 20170525-IGB-gcc-4.9.4-Python-2.7.13 Pylearn2 is a library designed to make machine learning research easy. - Homepage: https://github.com/lisa-lab/pylearn2
pymol 2.3.4 PyMOL is a user-sponsored molecular visualization system on an open-source foundation, maintained and distributed by Schrödinger.
pypy 7.3.5-IGB-gcc-4.9.4-Python-2.7.13 A fast, compliant alternative implementation of Python
PyRosetta 2021.25-IGB-gcc-8.2.0-Python-3.7.2 PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
Python 2.7.13-IGB-gcc-4.9.4
2.7.18-IGB-gcc-8.2.0
3.10.1-IGB-gcc-8.2.0
3.6.1-IGB-gcc-4.9.4
3.7.2-IGB-gcc-8.2.0 		Python is a programming language that lets you work more quickly and integrate your systems more effectively.
PyTorch 0.3.0-IGB-gcc-4.9.4-Python-3.6.1
0.4.0-IGB-gcc-4.9.4-Python-3.6.1
0.4.1-IGB-gcc-4.9.4-Python-2.7.13
1.0.1.post2-IGB-gcc-4.9.4-Python-3.6.1
1.11.0-IGB-gcc-8.2.0-Python-3.7.2
1.12.1-IGB-gcc-8.2.0-Python-3.10.1
1.12.1-IGB-gcc-8.2.0-Python-3.7.2
1.13.1-IGB-gcc-8.2.0-Python-3.7.2
1.3.1-IGB-gcc-4.9.4-Python-3.6.1
1.4.0-IGB-gcc-4.9.4-Python-3.6.1
1.6.0-IGB-gcc-4.9.4-Python-3.6.1
1.7.0-IGB-gcc-8.2.0-Python-3.7.2
1.9.0-IGB-gcc-8.2.0-Python-3.7.2 		Tensors and Dynamic neural networks in Pythonwith strong GPU acceleration.
pytorch-geometric 2.0.4-IGB-gcc-8.2.0-Python-3.7.2 PyG (PyTorch Geometric) is a library built upon PyTorch to easily write and train Graph Neural Networks (GNNs) for a wide range of applications related to structured data.
PyZMQ 16.0.2-IGB-gcc-4.9.4-Python-3.6.1 Python bindings for ZeroMQ
qgrs 1.0-IGB-gcc-4.9.4 C++ implementation of QGRS mapping algorithm - described here. This program differs from the actual algorithm used by QGRS Mapper recarding overlapping motifs and the maximum length of the motif.
QIIME 1.9.1 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
QIIME2 2017.10
2017.11
2017.12
2017.6
2017.8
2018.11
2018.2
2018.6
2018.8
2019.10
2019.4
2019.7
2020.2
2020.6
2020.8
2021.4
2022.8
2023.2
2023.7 		QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
Qt 4.8.7-IGB-gcc-4.9.4
4.8.7-IGB-gcc-8.2.0 		Qt is a comprehensive cross-platform C++ application framework.
qualimap 2.2.1-Java-1.8.0_121 Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts.
quast 4.6.1-IGB-gcc-4.9.4-Python-2.7.13
5.0.0-IGB-gcc-4.9.4-Python-3.6.1
5.0.2-IGB-gcc-8.2.0-Python-3.7.2 		QUAST performs fast and convenient quality evaluation and comparison of genome assemblies.
quickmerge 0.2-IGB-gcc-4.9.4-Python-2.7.13 quickmerge uses a simple concept to improve contiguity of genome assemblies based on long molecule sequences, often with dramatic outcomes. The program uses information from assemblies made with illumina short reads and PacBio long reads to improve contiguities of an assembly generated with PacBio long reads alone. This is counterintuitive because illumina short reads are not typically considered to cover genomic regions which PacBio long reads cannot. Although we have not evaluated this program for assemblies generated with Oxford nanopore sequences, the program should work with ONP-assemblies too.
R 2.15.3-IGB-gcc-4.9.4
3.1.2-IGB-gcc-4.9.4
3.2.5-IGB-gcc-4.9.4
3.3.3-IGB-gcc-4.9.4
3.4.1-IGB-gcc-4.9.4
3.4.2-IGB-gcc-4.9.4
3.5.0-IGB-gcc-4.9.4
3.6.0-IGB-gcc-8.2.0
4.0.3-IGB-gcc-8.2.0
4.1.2-IGB-gcc-8.2.0
4.2.2-IGB-gcc-8.2.0
4.3.2-IGB-gcc-8.2.0 		R is a free software environment for statistical computing and graphics.
racon 0.5.0-IGB-gcc-4.9.4-Python-2.7.13
0.5.0-IGB-gcc-4.9.4-Python-3.6.1
1.4.13-IGB-gcc-8.2.0 		Racon is intended as a standalone consensus module to correct raw contigs generated by rapid assembly methods which do not include a consensus step, such as Miniasm.The goal of Racon is to generate genomic consensus which is of similar or better quality compared to the output generated by assembly methods which employ both error correction and consensus steps, while providing a speedup of several times compared to those methods.
radar 1.3-IGB-gcc-8.2.0 Welcome to radar
radinitio 1.1.0-IGB-gcc-4.9.4-Python-3.6.1
1.1.1-IGB-gcc-4.9.4-Python-3.6.1 		RADinitio is a simulation pipeline for the assessment of RADseq experiments. Genetic data are forward simulated for a population of individuals from a designated reference genome.
Ragout 2.0-IGB-gcc-4.9.4 Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references.
RagTag 1.0.2-IGB-gcc-8.2.0-Python-3.7.2
1.1.1-IGB-gcc-8.2.0-Python-3.7.2 		RagTag, the successor to RaGOO, is a command line tool for reference-guided genome assembly improvement.
RAILS 1.5.1-IGB-gcc-8.2.0 RAILS and Cobbler are genomics application for scaffolding and automated finishing of genome assemblies with long DNA sequences. They can be used to scaffold & finish high-quality draft genome assemblies with any long, preferably high-quality, sequences such as scaftigs/contigs from another genome draft.
randfold 2.0.1-IGB-gcc-4.9.4 Minimum free energy of folding randomization test software
RAxML 8.2.12-IGB-gcc-4.9.4 RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
raxml-ng 1.2.0 RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.
rclone 1.41
1.52.3
1.60.0 		Rclone is a command line program to sync files and directories to and from different cloud storage
RcppGSL 0.3.2-IGB-gcc-4.9.4-R-3.3.3 Rcpp integration for GNU GSL vectors and matrices The GNU Scientific Library (or GSL) is a collection of numerical routines for scientific computing. It is particularly useful for C and C++ programs as it provides a standard C interface to a wide range of mathematical routines. There are over 1000 functions in total with an extensive test suite. The RcppGSL package provides an easy-to-use interface between GSL data structures and R using concepts from Rcpp which is itself a package that eases the interfaces between R and C++. This package also serves as a prime example of how to build a package that uses Rcpp to connect to another third-party library. The autoconf script, inline plugin and example package can all be used as a stanza to write a similar package against another library.
rdkit 2020_03_3-IGB-gcc-4.9.4-Python-3.6.1
2021_03_1-IGB-gcc-8.2.0-Python-3.7.2 		RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python.
RDPClassifier 2.12-Java-1.8.0_152
2.2-Java-1.8.0_152 		The RDP Classifier is a naive Bayesian classifier which was developed to provide rapid taxonomic placement based on rRNA sequence data. The RDP Classifier can rapidly and accurately classify bacterial and archaeal 16s rRNA sequences, and Fungal LSU sequences. It provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
READemption 1.0.1-IGB-gcc-8.2.0-Python-3.7.2 READemption is a pipeline for the computational evaluation of RNA-Seq data. It was originally developed to process dRNA-Seq reads (as introduced by Sharma et al., Nature, 2010 (Pubmed)) originating from bacterial samples.
REAP 1.2-IGB-gcc-8.2.0
REAPR 1.0.18-IGB-gcc-4.9.4 REAPR is a tool that evaluates the accuracy of a genome assembly using mapped paired end reads, without the use of a reference genome for comparison. It can be used in any stage of an assembly pipeline to automatically break incorrect scaffolds and flag other errors in an assembly for manual inspection. It reports mis-assemblies and other warnings, and produces a new broken assembly based on the error calls. - Homepage: http://www.sanger.ac.uk/science/tools/reapr
RECON 1.08-IGB-gcc-4.9.4-Perl-5.24.1 a package for automated de novo identification of repeat families from genomic sequences
redbiom 0.3.2-IGB-gcc-4.9.4-Python-3.6.1 Redbiom is a cache service for sample metadata and sample data.
RepeatMasker 4.0.7-IGB-gcc-4.9.4-Perl-5.24.1
4.0.7-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
4.1.1-IGB-gcc-4.9.4-Perl-5.24.1
4.1.2-p1-IGB-gcc-8.2.0-Perl-5.28.1 		RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
RepeatModeler 1.0.11-IGB-gcc-4.9.4-Perl-5.24.1
2.0.1-IGB-gcc-4.9.4-Perl-5.24.1
2.0.2a-IGB-gcc-4.9.4-Perl-5.24.1 		RepeatModeler is a de novo transposable element (TE) family identification and modeling package. At the heart of RepeatModeler are three de-novo repeat finding programs ( RECON, RepeatScout and LtrHarvest/Ltr_retriever ) which employ complementary computational methods for identifying repeat element boundaries and family relationships from sequence data.
RepeatScout 1.0.5-IGB-gcc-4.9.4 De Novo Repeat Finder,
reveal 0.2.2-IGB-gcc-4.9.4-Python-2.7.13 REVEAL (REcursiVe Exact-matching ALigner) can be used to (multi) align whole genomes.
RFMix 20180503-IGB-gcc-4.9.4 A discriminative method for local ancestry inference
rgeos 0.4-2-IGB-gcc-4.9.4-R-3.5.0 nterface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries.
RGT 0.11.3-IGB-gcc-4.9.4-Python-2.7.13 Regulatory Genomics Toolbox (RGT) is an open source python library for analysis of regulatory genomics. RGT is programmed in an oriented object fashion and its core classes provide functionality for handling regulatory genomics data.
rMATS 3.2.5-IGB-gcc-4.9.4-Python-2.7.13 MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. The statistical model of MATS calculates the P-value and false discovery rate that the difference in the isoform ratio of a gene between two conditions exceeds a given user-defined threshold. From the RNA-Seq data, MATS can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. MATS handles replicate RNA-Seq data from both paired and unpaired study design.
rMATS-turbo 4.1.1-IGB-gcc-8.2.0-Python-3.7.2 rMATS turbo is the C/Cython version of rMATS (refer to http://rnaseq-mats.sourceforge.net).
RMBlast 2.11.0-IGB-gcc-8.2.0
2.6.0-IGB-gcc-4.9.4
2.9.0-IGB-gcc-4.9.4 		RMBlast is a RepeatMasker compatible version of the standard NCBI blastn program. The primary difference between this distribution and the NCBI distribution is the addition of a new program "rmblastn" for use with RepeatMasker and RepeatModeler.
Rmpi 0.6-6-IGB-gcc-4.9.4-R-3.4.2 An interface (wrapper) to MPI APIs. It also provides interactive R manager and worker environment.
RNAhybrid 2.1.2-IGB-gcc-4.9.4 RNAhybrid is a tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, ie. the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.
RNAmmer 1.2-IGB-gcc-4.9.4-Perl-5.24.1
1.2-IGB-gcc-8.2.0-Perl-5.28.1 		Ribosomal RNA sub units
rnaquast 2.1.0-IGB-gcc-8.2.0-Python-3.7.2 rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
rnaseqtools 1.0.2-IGB-gcc-4.9.4 This repo rnaseqtools provides a set of tools to process transcripts (mainly in gtf format).
RNAstructure 6.0-IGB-gcc-4.9.4 RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities.
roary 3.13.0-IGB-gcc-4.9.4-Perl-5.24.1 Roary is a high speed stand alone pan genome pipeline, which takes annotated assemblies in GFF3 format (produced by Prokka (Seemann, 2014)) and calculates the pan genome.
rodeo2 2.4.2-IGB-gcc-8.2.0-Python-3.7.2 RODEO evaluates one or many genes, characterizing a gene neighborhood based on the presence of profile hidden Markov models (pHMMs).
root 6.14.06-IGB-gcc-4.9.4
6.14.06-IGB-gcc-4.9.4-Python-2.7.13 		A modular scientific software toolkit. It provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage. It is mainly written in C++ but integrated with other languages such as Python and R.
root-painter-trainer 0.2.19.1-IGB-gcc-8.2.0-Python-3.10.1 RootPainter is a GUI-based software tool for the rapid training of deep neural networks for use in biological image analysis. RootPainter uses a client-server architecture, allowing users with a typical laptop to utilise a GPU on a more computationally powerful server.
ROSE 20150210-IGB-gcc-4.9.4-Python-2.7.13 To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam)
rosetta 2017.52-IGB-gcc-4.9.4
3.12-IGB-gcc-4.9.4
3.13-IGB-gcc-8.2.0 		The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.
rpy 1.0.3-IGB-gcc-4.9.4-Python-2.7.13-R-2.15.3 RPy is a very simple, yet robust, Python interface to the R Programming Language. Itcan manage all kinds of R objects and can execute arbitrary R functionsincluding the graphic functions.
rpy2 2.8.6-IGB-gcc-4.9.4-Python-2.7.13-R-3.3.3
2.8.6-IGB-gcc-4.9.4-Python-2.7.13-R-3.5.0
2.9.0-IGB-gcc-4.9.4-Python-3.6.1-R-3.3.3
2.9.5-IGB-gcc-8.2.0-Python-3.7.2-R-4.1.2
3.0.1-IGB-gcc-4.9.4-Python-3.6.1-R-3.5.0
3.2.4-IGB-gcc-8.2.0-Python-3.7.2-R-3.6.0
3.4.5-IGB-gcc-8.2.0-Python-3.7.2-R-4.1.2 		rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions.
RREFinder 1.0.2-IGB-gcc-8.2.0-Python-3.7.2 Bioinformatic application for the detection of RREs in protein sequences of interest
RSAT 20230828-IGB-gcc-8.2.0 We offer tools to analyse cis-regulatory elements in genome sequences, motif discovery (support genome-wide data sets like ChIP-seq), transcription factor binding motif analysis (quality assessment, comparisons and clustering), comparative genomics, analysis of regulatory variations
RSEM 1.3.0-IGB-gcc-4.9.4
1.3.1-IGB-gcc-4.9.4
1.3.3-IGB-gcc-8.2.0 		RNA-Seq by Expectation-Maximization
RSeQC 2.6.4-IGB-gcc-4.9.4-Python-2.7.13 RSeQC package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
RStudio 2023.09.1-494 Used by millions of people weekly, the RStudio integrated development environment (IDE) is a set of tools built to help you be more productive with R and Python.
rtg-tools 3.8.4 RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats.
Ruby 2.4.2-IGB-gcc-4.9.4 Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
Rust 1.41.1 Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
sabre 20171114-IGB-gcc-4.9.4 Next-generation sequencing can currently produce hundreds of millions of reads per lane of sample and that number increases at a dizzying rate. Barcoding individual sequences for multiple lines or multiple species is a cost-efficient method to sequence and analyze a broad range of data.
SAI-app 20230425-IGB-gcc-8.2.0-Python-3.7.2 StomaAI application
Salmon 0.11.3-IGB-gcc-4.9.4
0.12.0-IGB-gcc-8.2.0
0.13.1-IGB-gcc-8.2.0
0.14.1-IGB-gcc-8.2.0
0.8.2-IGB-gcc-4.9.4-Python-2.7.13
0.9.1-IGB-gcc-4.9.4
1.0.0-IGB-gcc-8.2.0
1.1.0-IGB-gcc-8.2.0
1.10.0-IGB-gcc-8.2.0
1.2.1-IGB-gcc-8.2.0
1.4.0-IGB-gcc-8.2.0
1.5.2-IGB-gcc-8.2.0 		Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
SalmonTE 0.4-IGB-gcc-8.2.0 SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances from Next Generation Sequencing Data.
SalmonTools 20190604-IGB-gcc-8.2.0 Useful tools for working with Salmon output
SALSA 2.2-IGB-gcc-4.9.4-Python-2.7.13
2.3-IGB-gcc-4.9.4-Python-2.7.13 		A tool to scaffold long read assemblies with Hi-C
salt beta0.2-IGB-gcc-8.2.0 alignment algorithm that is SNP-aware
sambamba 0.6.6
0.8.0 		sambamba view allows to efficiently filter SAM/BAM/CRAM files for alignments satisfying various conditions, as well as access its SAM header and information about reference sequences.
samblaster 0.1.24-IGB-gcc-4.9.4 ummary samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files. It can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs.
SAMtools 0.1.18-IGB-gcc-4.9.4
0.1.20-IGB-gcc-4.9.4
0.1.20-IGB-gcc-8.2.0
1.10-IGB-gcc-8.2.0
1.11-IGB-gcc-8.2.0
1.12-IGB-gcc-8.2.0
1.17-IGB-gcc-8.2.0
1.3.1-IGB-gcc-4.9.4
1.4-IGB-gcc-4.9.4
1.4.1-IGB-gcc-4.9.4
1.5-IGB-gcc-4.9.4
1.7-IGB-gcc-4.9.4
1.9-IGB-gcc-4.9.4 		SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
sbanalyzer 3.0-14
3.1-2 		Shoreline Biome’s unique microbiome kits are the key to generating long-read next-generation sequencing data necessary to discriminate microbial strains from any sample.
ScaLAPACK The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
scallop 0.10.3-IGB-gcc-4.9.4
0.10.4-IGB-gcc-4.9.4 		Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.
scikit-cuda 0.5.1-IGB-gcc-4.9.4-Python-2.7.13 scikit-cuda provides Python interfaces to many of the functions in the CUDA device/runtime, CUBLAS, CUFFT, and CUSOLVER libraries distributed as part of NVIDIAs CUDA Programming Toolkit, as well as interfaces to select functions in the free and standard versions of the CULA Dense Toolkit. Both low-level wrapper functions similar to their C counterparts and high-level functions comparable to those in NumPy and Scipy are provided.
scoary 1.6.16-IGB-gcc-4.9.4-Python-3.6.1 Scoary is designed to take the gene_presence_absence.csv file from Roary as well as a traits file created by the user and calculate the assocations between all genes in the accessory genome and the traits. It reports a list of genes sorted by strength of association per trait.
SCons 3.0.1-IGB-gcc-4.9.4-Python-2.7.13
3.0.1-IGB-gcc-4.9.4-Python-3.6.1 		SCons is a software construction tool.
scrappie 1.3.0-IGB-gcc-4.9.4 Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group.
SDL2 2.0.4-IGB-gcc-4.9.4 SDL: Simple DirectMedia Layer, a cross-platform multimedia library
segemehl 0.3.4-IGB-gcc-8.2.0 segemehl is a software to map short sequencer reads to reference genomes. segemehl implements a matching strategy based on enhanced suffix arrays (ESA)
Segway 2.0.1-IGB-gcc-4.9.4-Python-2.7.13 Segway is a tool for easy pattern discovery and identification in functional genomics data.
sentieon 201808
201911
202010.01
202112
202112.01
202112.04
202112.06
202308
202308.02 		A fast and accurate solution to variant calling from next-generation sequence data
SEPP 20180223-IGB-gcc-4.9.4-Python-2.7.13
4.3.10-IGB-gcc-8.2.0-Python-3.7.2
4.5.1-IGB-gcc-8.2.0-Python-3.7.2 		SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
seqan 2.2.0-IGB-gcc-8.2.0
2.3.2-IGB-gcc-4.9.4 		SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data
seqkit 0.12.1
0.15.0
2.0.0
2.3.0
2.5.1
2.6.1 		a cross-platform and ultrafast toolkit for FASTA/Q file manipulation
SeqLib C++ interface to HTSlib, BWA-MEM and Fermi
SeqPrep 1.3.2-IGB-gcc-8.2.0 SeqPrep is a program to merge paired end Illumina reads that are overlapping into a single longer read. It may also just be used for its adapter trimming feature without doing any paired end overlap.
seqtk 1.2-IGB-gcc-4.9.4
1.2-IGB-gcc-8.2.0
1.3-IGB-gcc-8.2.0 		Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
SequelTools 20200619-IGB-gcc-8.2.0-Python-3.7.2 SequelTools is a fast and easy to install command-line program that provides a collection of tools for working with multiple SMRTcells of BAM format PacBio Sequel raw sequece data.
shapeit 2.20 SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
sharutils 4.15.2-IGB-gcc-4.9.4 GNU shar makes so-called shell archives out of many files, preparing them for transmission by electronic mail services, while unshar helps unpacking shell archives after reception.
shasta 0.2.0 The goal of the Shasta long read assembler is to rapidly produce accurate assembled sequence using as input DNA reads generated by Oxford Nanopore flow cells.
shortbred 0.9.5-IGB-gcc-4.9.4-Python-2.7.13 ShortBRED is a pipeline to take a set of protein sequences, reduce them to a set of unique identifying strings ("markers"), and then search for these markers in metagenomic data and determine the presence and abundance of the protein families of interest.
Sibelia 3.0.7-IGB-gcc-4.9.4 Sibelia is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species.
sickle 1.33-IGB-gcc-8.2.0 A windowed adaptive trimming tool for FASTQ files using quality
SignalP 4.1 Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
simba 1.3.0 The SimBA region of interest (ROI) interface allows users to define and draw ROIs on videos. ROI data can be used to calculate basic descriptive statistics based on animals movements and locations such as:
singularity 3.4.1
3.8.1 		Application and environment virtualization
skylign 1.1-IGB-gcc-4.9.4-Perl-5.24.1 Skylign is a tool for creating logos representing both sequence alignments and profile hidden Markov models. Submit to the form on the right in order to produce (i) interactive logos for inclusion in webpages, or (ii) static logos for use in documents.
sleap 1.2.4-IGB-gcc-8.2.0-Python-3.7.2 SLEAP is an open source deep-learning based framework for multi-animal pose tracking. It can be used to track any type or number of animals and includes an advanced labeling/training GUI for active learning and proofreading.
SMART-Aptamer-v1 20200313-IGB-gcc-4.9.4
SMART-Aptamer-v2 20200315-IGB-gcc-4.9.4
SMARTdenovo 20170916-IGB-gcc-4.9.4-Perl-5.24.1 SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy.
smrtlink 10.0.0.108728
11.0.0.146107
11.1.0.166339
8.0.0.80529
9.0.0.92188 		PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface.
smudgeplot 0.2.5-IGB-gcc-8.2.0-Python-3.7.2 This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them.
snakemake 6.0.5-IGB-gcc-8.2.0-Python-3.7.2 The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. Workflows are described via a human readable, Python based language.
SNAP 2013-11-29-IGB-gcc-4.9.4 (Semi-HMM-based Nucleic Acid Parser) gene prediction tool
snapgene-reader 0.1.19-IGB-gcc-8.2.0-Python-3.7.2 SnapGene Reader is a Python library to parse Snapgene *.dna files into dictionaries or Biopython SeqRecords
Sniffles 1.0.12b-IGB-gcc-8.2.0 Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.
snoscan 0.9.1-IGB-gcc-4.9.4-Perl-5.24.1
0.9.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded 		Search for C/D box methylation guide snoRNA genes in a genomic sequence
snpEff 4.3o-Java-1.8.0_121
4.3t-Java-1.8.0_152
5.0e-Java-15.0.1
5.1f-Java-15.0.1 		SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes).
snpomatic 1.0-IGB-gcc-4.9.4 SNP-o-matic is a fast, stringent short-read mapping software. It supports a multitude of output types and formats, for uses in filtering reads, alignments, sequence-based genotyping calls, assisted reassembly of contigs etc.
SNPsplit 0.6.0-IGB-gcc-8.2.0-Perl-5.28.1 SNPsplit is an allele-specific alignment sorter which is designed to read alignment files in SAM/BAM format and determine the allelic origin of reads that cover known SNP positions.
SNVer 0.5.3-Java-1.8.0_121
0.5.3-Java-1.8.0_152 		SNVer is a statistical tool for calling common and rare variants in analysis of pool or individual next-generation sequencing data. It reports one single overall p-value for evaluating the significance of a candidate locus being a variant, based on which multiplicity control can be obtained.
SOAPdenovo-Trans 1.03 SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.
SOAPdenovo2 r242-IGB-gcc-8.2.0 SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes. The program is specially designed to assemble Illumina GA short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.
songbird 1.0.3-IGB-gcc-4.9.4-Python-3.6.1 Establishing microbial composition measurement standards with reference frames
sortmerna 2.1
4.3.6 		SortMeRNA is a program tool for filtering, mapping and OTU-picking NGS reads in metatranscriptomic and metagenomic data. The core algorithm is based on approximate seeds and allows for fast and sensitive analyses of nucleotide sequences.
sourcetracker 2.0.1-IGB-gcc-4.9.4-Python-3.6.1 Bayesian community-wide culture-independent microbial source tracking
sourmash 4.6.1-IGB-gcc-8.2.0-Python-3.10.1 Quickly search, compare, and analyze genomic and metagenomic data sets.
SoX 14.4.2-IGB-gcc-4.9.4 Sound eXchange, the Swiss Army knife of audio manipulation
spaceranger 1.0.0
1.1.0
1.2.2
1.3.0
2.0.0
2.1.0 		Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield and fluorescence microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image.
spaCy 2.3.2-IGB-gcc-4.9.4-Python-3.6.1 spaCy is designed to help you do real work — to build real products, or gather real insights. The library respects your time, and tries to avoid wasting it. It's easy to install, and its API is simple and productive.
SPAdes 3.10.1-IGB-gcc-4.9.4-Python-2.7.13
3.11.0-IGB-gcc-4.9.4-Python-2.7.13
3.11.0-IGB-gcc-4.9.4-Python-3.6.1
3.11.1-IGB-gcc-4.9.4-Python-3.6.1
3.13.1-IGB-gcc-8.2.0-Python-3.7.2
3.14.1-IGB-gcc-8.2.0-Python-3.7.2
3.15.0-IGB-gcc-8.2.0-Python-3.7.2
3.15.3-IGB-gcc-8.2.0-Python-3.7.2
3.15.5-IGB-gcc-8.2.0-Python-3.7.2 		SPAdes . St. Petersburg genome assembler . is intended for both standard isolates and single-cell MDA bacteria assemblies.
sparsehash 2.0.3-IGB-gcc-4.9.4
2.0.3-IGB-gcc-8.2.0 		This directory contains several hash-map implementations, similar inAPI to SGIs hash_map class, but with different performance characteristics.
Spine 0.2.1-IGB-gcc-4.9.4 Spine identifies a core genome from input genomic sequences. Sequences are aligned using Nucmer and regions found to be in common between all or a user-defined subset of genomes will be returned.
SQLite 3.17.0-IGB-gcc-4.9.4
3.17.0-IGB-gcc-8.2.0
3.30.1-IGB-gcc-4.9.4 		SQLite: SQL Database Engine in a C Library
squid 1.9g-IGB-gcc-4.9.4 A C library that is bundled with much of the above software. C function library for sequence analysis.
SRA-Toolkit 2.10.5
2.10.9
2.8.2-1
3.0.0 		The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format
ssaha2 2.5.5-IGB-gcc-4.9.4 SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.
ssaha_pileup 0.6-IGB-gcc-4.9.4 SSAHA2: Sequence Search and Alignment by Hashing Algorithm
SSW SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically.
Stacks 1.47-IGB-gcc-4.9.4
2.54-IGB-gcc-8.2.0
2.62-IGB-gcc-8.2.0 		Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
STAR 2.5.3a-IGB-gcc-4.9.4
2.6.0c-IGB-gcc-4.9.4
2.6.1b-IGB-gcc-4.9.4
2.7.0d-IGB-gcc-8.2.0
2.7.0f-IGB-gcc-8.2.0
2.7.10a-IGB-gcc-8.2.0
2.7.3a-IGB-gcc-8.2.0
2.7.4a-IGB-gcc-8.2.0
2.7.6a-IGB-gcc-8.2.0 		STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
STAR-Fusion 1.6.0-IGB-gcc-4.9.4 STAR-Fusion is a component of the Trinity Cancer Transcriptome Analysis Toolkit (CTAT). STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads.
strauto 1-IGB-gcc-4.9.4 Automation and Parallelization of STRUCTURE Analysis
strelka 2.9.9 Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
StringTie 1.3.3-IGB-gcc-4.9.4
1.3.6-IGB-gcc-4.9.4 		StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
stringtie 2.1.1-IGB-gcc-4.9.4 Transcript assembly and quantification for RNA-Seq
structure 2.3.4-IGB-gcc-4.9.4 The program structure is a free software package for using multi-locus genotype data to investigate population structure.
Subread 1.5.2-IGB-gcc-4.9.4
1.6.3-IGB-gcc-4.9.4
2.0.0-IGB-gcc-8.2.0
2.0.4-IGB-gcc-8.2.0 		High performance read alignment, quantification and mutation discovery
SuiteSparse 5.4.0-IGB-gcc-4.9.4-METIS-5.1.0
5.8.1-IGB-gcc-8.2.0 		SuiteSparse is a collection of libraries manipulate sparse matrices.
SUNDIALS 2.6.2-IGB-gcc-4.9.4 SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
Supernova 1.1.5
1.2.0
1.2.1
2.0.0
2.0.1
2.1.0
2.1.1 		Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source. A key feature of Supernova is that it creates diploid assemblies, thus separately representing maternal and paternal chromosomes over very long distances.
SURVIVOR 1.0.7-IGB-gcc-8.2.0 SURVIVOR is a tool set for simulating/evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs.
svtools 0.5.1-IGB-gcc-4.9.4-Python-2.7.13 Comprehensive utilities to explore structural variations in genomes
svtyper 0.7.1-IGB-gcc-4.9.4-Python-2.7.13 SVTyper performs breakpoint genotyping of structural variants (SVs) using whole genome sequencing data.
swift-t 1.3-IGB-gcc-4.9.4 Swift/T is a completely new implementation of the Swift language for high-performance computing. In this implementation, the Swift script is translated into an MPI program that uses the Turbine (hence, /T) and ADLB runtime libraries for highly scalable dataflow processing over MPI, without single-node bottlenecks.
SWIG 2.0.12-IGB-gcc-4.9.4-Python-2.7.13
3.0.12-IGB-gcc-4.9.4-Python-2.7.13
3.0.12-IGB-gcc-4.9.4-Python-2.7.13-Perl-5.24.1 		SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. - Homepage: http://www.swig.org/
synapseclient 1.9.2-IGB-gcc-4.9.4-Python-3.6.1 Synapse is an open source software platform that data scientists can use to carry out, track, and communicate their research in real time.
Szip Szip compression software, providing lossless compression of scientific data
t3f 1.1.0-IGB-gcc-4.9.4-Python-3.6.1
1.1.0-IGB-gcc-4.9.4-Python-3.6.1-TF-2.0.3
20200316-IGB-gcc-4.9.4-Python-3.6.1-TF-2.0.3
20200316-IGB-gcc-4.9.4-Python-3.6.1-TF-2.2.0 		t3f is a library for working with Tensor Train decomposition.
tabix 0.2.6-IGB-gcc-4.9.4 Generic indexer for TAB-delimited genome position files
tabixpp 1.1.0-IGB-gcc-8.2.0 This is a C++ wrapper around tabix project which abstracts some of the details of opening and jumping in tabix-indexed files.
tagdigger 1.1-IGB-gcc-4.9.4-Python-3.6.1 TagDigger is a program for processing FASTQ files from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) experiments.
tailseeker 3.2.1 Tailseeker is the official pipeline for TAIL-seq, which measures poly(A) tail lengths and 3′-end modifications with Illumina SBS sequencers.
TAPE 0.4-IGB-gcc-4.9.4-Python-3.6.1
20191209-IGB-gcc-4.9.4-Python-3.6.1 		Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.
tar 1.32-IGB-gcc-8.2.0 tar: The GNU tape archiver
TASSEL 5.2.28-Java-1.8.0_121
5.2.28-Java-1.8.0_152 		While TASSEL has changed considerably since its initial public release in 2001, its primary function continues to be providing tools to investigate the relationship between phenotypes and genotypes
tbb Intel Threading Building Blocks 4.0 (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms.
tbl2asn 20180516
20190117
20200203
20200707 		Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank
Tcl Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language,suitable for a very wide range of uses, including web and desktop applications, networking, administration,testing and many more.
tensorboardX 1.9-IGB-gcc-4.9.4-Python-3.6.1
2.0-IGB-gcc-4.9.4-Python-3.6.1
2.1-IGB-gcc-8.2.0-Python-3.7.2
2.5.1-IGB-gcc-8.2.0 		Tensorboard for PyTorch.
Tensorflow 1.15.2-IGB-gcc-4.9.4-Python-3.6.1
1.2.1-IGB-gcc-4.9.4-Python-2.7.13
2.2.0-IGB-gcc-4.9.4-Python-3.6.1
2.8.2-IGB-gcc-8.2.0-Python-3.7.2
2.9.1-IGB-gcc-8.2.0-Python-3.7.2 		An open-source software library for Machine Intelligence
Tensorflow-GPU 1.13.1-IGB-gcc-4.9.4-Python-3.6.1
1.14.0-IGB-gcc-4.9.4-Python-3.6.1
1.2.1-IGB-gcc-4.9.4-Python-3.6.1
1.5.1-IGB-gcc-4.9.4-Python-3.6.1
1.9.0-IGB-gcc-4.9.4-Python-3.6.1
2.0.3-IGB-gcc-4.9.4-Python-3.6.1
2.11.0-IGB-gcc-8.2.0-Python-3.7.2
2.2.0-IGB-gcc-4.9.4-Python-3.6.1
2.3.1-IGB-gcc-8.2.0-Python-3.7.2
2.5.3-IGB-gcc-8.2.0-Python-3.7.2
2.6.5-IGB-gcc-8.2.0-Python-3.7.2
2.9.1-IGB-gcc-8.2.0-Python-3.7.2 		An open-source software library for Machine Intelligence
TensorFlowModels 1.11-IGB-gcc-4.9.4-Python-3.6.1
20171113-IGB-gcc-4.9.4-Python-3.6.1 		This repository contains a number of different models implemented in TensorFlow:
tensorly 0.4.2-IGB-gcc-4.9.4-Python-3.6.1 Simple and Fast Tensor Learning in Python
TEtranscripts 2.2.1-IGB-gcc-8.2.0-Python-3.7.2 TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements. TEtranscripts then performs differential analysis using DESeq2.
Tk Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
TMHMM 2.0c Prediction of transmembrane helices in proteins
toil 5.3.0-IGB-gcc-8.2.0-Python-3.7.2 Toil is a scalable, efficient, cross-platform (Linux & macOS) pipeline management system, written entirely in Python, and designed around the principles of functional programming.
tolkein 0.2.6-IGB-gcc-4.9.4-Python-3.6.1 Tree of Life Kit of Evolutionary Informatics Novelties
tombo 1.5-IGB-gcc-4.9.4-Python-3.6.1 Tombo is a suite of tools primarily for the identification of modified nucleotides from nanopore sequencing data. Tombo also provides tools for the analysis and visualization of raw nanopore signal.
TopHat 1.4.1
2.1.1-IGB-gcc-4.9.4 		TopHat is a fast splice junction mapper for RNA-Seq reads.
Torch 20171018-IGB-gcc-4.9.4-Python-3.6.1 Torch is a scientific computing framework with wide support for machine learning algorithms that puts GPUs first. It is easy to use and efficient, thanks to an easy and fast scripting language, LuaJIT, and an underlying C/CUDA implementation.
torchsample 0.1.3-IGB-gcc-4.9.4-Python-3.6.1 High-Level Training, Data Augmentation, and Utilities for Pytorch
TransDecoder 5.1.0-IGB-gcc-4.9.4-Perl-5.24.1
5.5.0-IGB-gcc-4.9.4-Perl-5.24.1
5.7.0-IGB-gcc-8.2.0-Perl-5.28.1 		TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
transrate 1.0.3 Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies.
tre 20161208-IGB-gcc-4.9.4 TRE is a lightweight, robust, and efficient POSIX compliant regexp matching library with some exciting features such as approximate (fuzzy) matching.The matching algorithm used in TRE uses linear worst-case time in the length of the text being searched, and quadratic worst-case time in the length of the used regular expression.In other words, the time complexity of the algorithm is O(M^2N), where M is the length of the regular expression and N is the length of the text. The used space is also quadratic on the length of the regex, but does not depend on the searched string. This quadratic behaviour occurs only on pathological cases which are probably very rare in practice.
treemix 1.13-IGB-gcc-4.9.4 TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. In the underlying model, the modern-day populations in a species are related to a common ancestor via a graph of ancestral populations. We use the allele frequencies in the modern populations to infer the structure of this graph.
trf 4.0.9 Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
Trimmomatic 0.33-Java-1.8.0_152
0.36-Java-1.8.0_152
0.38-Java-1.8.0_152
0.39-Java-1.8.0_201 		Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
Trim_Galore 0.4.4-IGB-gcc-4.9.4
0.6.5-IGB-gcc-4.9.4 		A wrapper tool around Cutadapt and FastQC to consistently apply quality and adapter trimming to FastQ files, with some extra functionality for MspI-digested RRBS-type (Reduced Representation Bisufite-Seq) libraries.
Trinity 2.10.0-IGB-gcc-8.2.0
2.14.0-IGB-gcc-8.2.0
2.15.1-IGB-gcc-8.2.0
2.4.0-IGB-gcc-4.9.4
2.5.0-IGB-gcc-4.9.4
2.6.5-IGB-gcc-4.9.4
2.8.5-IGB-gcc-4.9.4 		Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
Trinotate 3.1.1-IGB-gcc-4.9.4-Perl-5.24.1
3.2.1-IGB-gcc-4.9.4-Perl-5.24.1
4.0.0-IGB-gcc-8.2.0-Perl-5.28.1 		Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome.
tRNAscan-SE 1.3.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded tRNAscan-SE: a tool for finding transfer RNAs
truesight 0.06-IGB-gcc-4.9.4 A Self-training Algorithm for Splice Junction Detection using RNA-seq.
Trycycler 0.4.1-IGB-gcc-8.2.0-Python-3.7.2 Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs.
TSEBRA 1.0.3-IGB-gcc-8.2.0 TSEBRA is a combiner tool that selects transcripts from gene predictions based on the support by extrisic evidence in form of introns and start/stop codons. It was developed to combine BRAKER11 and BRAKER22 predicitons to increase their accuracies.
TULIP 20170513-IGB-gcc-4.9.4-Perl-5.24.1 Tulipseed takes as input alignments files of long reads to sparse short seeds, and outputs a graph and scaffold structures. Tulipbulb adds long read sequencing data to these.
udunits UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
ukbiobank 20190130 Biobank download software
umap-learn 0.4.6-IGB-gcc-4.9.4-Python-3.6.1
0.4.6-IGB-gcc-8.2.0-Python-3.7.2
0.5.2-IGB-gcc-8.2.0-Python-3.7.2 		Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction.
umi-tools 1.0.1-IGB-gcc-8.2.0-Python-3.7.2 Tools for handling Unique Molecular Identifiers in NGS data sets
unanimity 20180307-IGB-gcc-4.9.4 C++ library and its applications to generate and process accurate consensus sequences
Unicycler 0.4.3-IGB-gcc-4.9.4-Python-3.6.1
0.4.4-IGB-gcc-4.9.4-Python-3.6.1
0.4.8-IGB-gcc-4.9.4-Python-3.6.1 		Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.
unirep 20200303-IGB-gcc-4.9.4-Python-3.6.1 UniRep, a mLSTM "babbler" deep representation learner for protein engineering informatics.
unrar 5.7.3-IGB-gcc-4.9.4 RAR is a powerful archive manager.
USEARCH 11.0.667
11.0.667-akent
6.1.544
7.0.1090
9.2.64 		USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
util-linux 2.34-IGB-gcc-4.9.4 Set of Linux utilities
valgrind 3.13.0-IGB-gcc-4.9.4 Valgrind is an instrumentation framework for building dynamic analysis tools. There are Valgrind tools that can automatically detect many memory management and threading bugs, and profile your programs in detail. You can also use Valgrind to build new tools.
variscan 2.0.3-IGB-gcc-4.9.4 VariScan is a software package for the analysis of DNA sequence polymorphisms at the whole genome scale. Among other features,
VarScan 2.3.9-Java-1.8.0_152
vartrix 1.1.22 VarTrix is a software tool for extracting single cell variant information from 10x Genomics single cell data. VarTrix will take a set of previously defined variant calls and use that to identify those variants in the single cell data.
VASP-E 20190225-IGB-gcc-4.9.4
20191112-IGB-gcc-4.9.4 		VASP and VASP-E explore the idea that a solid geometric representation of molecular structures can be used to automatically deconstruct proteins into functional elements for the study of binding specificity.
vcfCodingSnps 1.5 vcfCodingSnps is a SNP annotation tool that annotates coding variants in VCF files.
vcflib 1.0.0-rc2-IGB-gcc-8.2.0
1.0.2-IGB-gcc-8.2.0 		a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
VCFtools 0.1.15-IGB-gcc-4.9.4-Perl-5.24.1
0.1.16-IGB-gcc-8.2.0-Perl-5.28.1 		The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
velocyto 0.17.17-IGB-gcc-4.9.4-Python-3.6.1 Velocyto is a library for the analysis of RNA velocity.
velocyto.R 20190527-IGB-gcc-4.9.4-R-3.4.2 RNA velocity estimation in R
velvet 1.2.10-IGB-gcc-4.9.4-kmer_121
1.2.10-IGB-gcc-8.2.0-kmer_121 		Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near Cambridge, in the United Kingdom.
VEP 92.4-IGB-gcc-4.9.4-Perl-5.24.1 VEP (Variant Effect Predictor) predicts the functional effects of genomic variants.
vg 1.15.0 variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
VICSIN 0.5-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13
0.5.1-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13
0.5.2-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13
1.0-IGB-gcc-4.9.4-Perl-5.24.1-Python-2.7.13
dev 		VICSIN = Viral, Integrative, and Conjugative Sequence Identification and Networking
ViennaRNA 2.4.14-IGB-gcc-4.9.4
2.4.2-IGB-gcc-4.9.4 		The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
VirSorter 20170215-IGB-gcc-4.9.4-Perl-5.24.1 VirSorter: mining viral signal from microbial genomic data.
VirSorter2 2.2.3 irSorter2 applies a multi-classifier, expert-guided approach to detect diverse DNA and RNA virus genomes.
virulencefinder 2.0.4-IGB-gcc-8.2.0-Python-3.7.2 The VirulenceFinder service contains one python script virulencefinder.py which is the script of the latest version of the VirulenceFinder service. VirulenceFinder identifies viruelnce genes in total or partial sequenced isolates of bacteria - at the moment only E. coli, Enterococcus, S. aureus and Listeria are available.
VMD 1.9.3-IGB-gcc-4.9.4
1.9.4a38-IGB-gcc-8.2.0 		VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.
VSEARCH 2.4.3-IGB-gcc-4.9.4 VSEARCH stands for vectorized search, as the tool takes advantage of parallelism in the form of SIMD vectorization as well as multiple threads to perform accurate alignments at high speed. - Homepage: https://github.com/torognes/vsearch
weblogo 3.7.12-IGB-gcc-8.2.0-Python-3.10.1 WebLogo is a web-based application designed to make the generation of sequence logos easy and painless. WebLogo has been featured in over 10000 scientific publications.
whatshap 1.0-IGB-gcc-8.2.0-Python-3.7.2 WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
wombat 20210107 WOMBAT is a program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML).
wtdbg2 2.3-IGB-gcc-4.9.4
2.5-IGB-gcc-4.9.4 		Wtdbg2 is a de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies (ONT). It assembles raw reads without error correction and then builds the consensus from intermediate assembly output.
wxPython 4.1.0-IGB-gcc-4.9.4-Python-3.6.1
4.1.0-IGB-gcc-8.2.0-Python-3.7.2 		the cross-platform GUI toolkit for the Python language. With wxPython software developers can create truly native user interfaces for their Python applications, that run with little or no modifications on Windows, Macs and Linux or other unix-like systems.
x264 x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.
xgboost 0.80-IGB-gcc-4.9.4-Python-3.6.1 XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. It implements machine learning algorithms under the Gradient Boosting framework.
xorg-macros X.org macros utilities.
xpore 2.1-IGB-gcc-8.2.0-Python-3.10.1 xPore is a Python package for identification of differentail RNA modifications from Nanopore sequencing data.
xTea 0.1.6 xTea (comprehensive transposable element analyzer) is designed to identify TE insertions from paired-end Illumina reads, barcode linked-reads, long reads (PacBio or Nanopore), or hybrid data from different sequencing platforms and takes whole-exome sequencing (WES) or whole-genome sequencing (WGS) data as input.
XZ 5.2.3-IGB-gcc-4.9.4
5.2.3-IGB-gcc-8.2.0 		xz: XZ utilities
yahs 1.2a.2-IGB-gcc-8.2.0 YaHS is a scaffolding tool using Hi-C data. It relies on a new algothrim for contig joining detection which considers the topological distribution of Hi-C signals aiming to distingush real interaction signals from mapping nosies.
Yasm Yasm: Complete rewrite of the NASM assembler with BSD license
ZeroMQ ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It is fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.
zlib zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system.
zorro 20111201 A probabilistic alignment masking program
zstd 1.4.4-IGB-gcc-4.9.4
1.5.5-IGB-gcc-8.2.0 		Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.
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