Difference between revisions of "Biocluster Applications"

From Carl R. Woese Institute for Genomic Biology - University of Illinois Urbana-Champaign
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!Installed Versions
 
!Installed Versions
 
!Description
 
!Description
 +
|-
 +
|[http://454.com/products/analysis-software/index.asp 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
 
|-
 
|-
 
|[http://www.bcgsc.ca/platform/bioinfo/software/abyss ABySS]
 
|[http://www.bcgsc.ca/platform/bioinfo/software/abyss ABySS]
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|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://gnuplot.sourceforge.net/ gnuplot]
+
|[https://projects.coin-or.org/ADOL-C ADOL-C]
−
|4.6.7-IGB-gcc-4.9.4<br>5.0.6-IGB-gcc-4.9.4
+
|2.6.3-IGB-gcc-4.9.4
−
|Portable interactive, function plotting utility - Homepage: http://gnuplot.sourceforge.net/
+
|ADOL-C is an open-source package for the automatic differentiation of C and C++ programs.  
 
|-
 
|-
−
|[https://github.com/simroux/VirSorter VirSorter]
+
|[http://vfsmspineagent.fsm.northwestern.edu/ AGEnt]
−
|20170215-IGB-gcc-4.9.4-Perl-5.24.1
+
|0.2.1-IGB-gcc-4.9.4
−
|VirSorter: mining viral signal from microbial genomic data.
+
|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://github.com/DecodeGenetics/graphtyper graphtyper]
+
|[https://github.com/martinwu/AMPHORA2 AMPHORA2]
−
|1.3-IGB-gcc-4.9.4
+
|20190104-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.
+
|An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
 
|-
 
|-
−
|M4
+
|ANTLR
 
|
 
|
−
|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
+
|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.
 
|-
 
|-
−
|[https://sites.google.com/site/danposdoc/news DANPOS]
+
|[https://github.com/bcgsc/arcs ARCS]
−
|2.2.2-IGB-gcc-4.9.4-Python-2.7.13-R-3.3.3
+
|1.0.0-IGB-gcc-4.9.4-Perl-5.24.1
−
|A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2
+
|Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. - Homepage: https://github.com/bcgsc/arcs
 
|-
 
|-
−
|[https://github.com/torognes/vsearch VSEARCH]
+
|ATK
−
|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
+
|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://xianyi.github.com/OpenBLAS/ OpenBLAS]
+
|[http://bioinf.uni-greifswald.de/augustus/ AUGUSTUS]
−
|0.2.19-GCC-4.9.4-2.28-LAPACK-3.7.0-test
+
|3.3-IGB-gcc-4.9.4
−
|OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
+
|AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
 
|-
 
|-
−
|[https://github.com/rrwick/Porechop Porechop]
+
|[https://github.com/MikkelSchubert/adapterremoval AdapterRemoval]
−
|0.2.3-IGB-gcc-4.9.4-Python-3.6.1
+
|2.1.7-IGB-gcc-4.9.4
−
|Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.
+
|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://www.gnu.org/software/gperf/ gperf]
+
|[https://github.com/DReichLab/AdmixTools AdmixTools]
−
|3.1-IGB-gcc-4.9.4
+
|1.0.1-IGB-gcc-4.9.4
−
|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.  
+
|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://guidance.tau.ac.il/ver2/ GUIDANCE]
+
|[https://github.com/baoe/AlignGraph AlignGraph]
−
|2.02-IGB-gcc-4.9.4-Perl-5.24.1
+
|20180222-IGB-gcc-4.9.4
−
|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/
+
|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://dna.ku.dk/%7Esapfo/bammds.html bammds]
+
|[https://www.continuum.io/anaconda-overview Anaconda2]
−
|20140602-IGB-gcc-4.9.4
+
|4.3.1
−
|Software that allows to create a multidimensional scaling (MDS) plot of populations for genetic 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. - Homepage: https://www.continuum.io/anaconda-overview
 +
|-
 +
|[https://www.continuum.io/anaconda-overview Anaconda3]
 +
|2019.10<br>5.0.1<br>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.
 
|-
 
|-
−
|[http://www.littlecms.com/ LittleCMS]
+
|[https://github.com/mgbellemare/Arcade-Learning-Environment ArcadeLearningEnvironment]
−
|2.8-IGB-gcc-4.9.4
+
|0.5.1-IGB-gcc-4.9.4-Python-2.7.13
−
|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/
+
|The Arcade Learning Environment (ALE) -- a platform for AI research. - Homepage: https://github.com/mgbellemare/Arcade-Learning-Environment
 
|-
 
|-
−
|[https://github.com/adrianlopezroche/fdupes fdupes]
+
|[http://assemblytics.com/ Assemblytics]
−
|1.6.1-IGB-gcc-4.9.4
+
|3f570cd-IGB-gcc-4.9.4<br>df5361f-IGB-gcc-4.9.4
−
|FDUPES is a program for identifying duplicate files residingwithin specified directories.
+
|Analyze your assembly by comparing it to a reference genome
 
|-
 
|-
−
|cairo
+
|Autoconf
 
|
 
|
−
|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
+
|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.bx.psu.edu/~rsharris/lastz/ LASTZ]
+
|Automake
−
|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/
+
|Automake: GNU Standards-compliant Makefile generator
 
|-
 
|-
−
|[http://lasagne.readthedocs.io/en/latest/index.html Lasagne]
+
|Autotools
−
|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
+
|This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
 
|-
 
|-
−
|[http://prinseq.sourceforge.net/ prinseq]
+
|[https://jgi.doe.gov/data-and-tools/bbtools/ BBMap]
−
|0.20.4-IGB-gcc-4.9.4-Perl-5.24.1
+
|38.36-Java-1.8.0_152
−
|PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data.  
+
|BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
 
|-
 
|-
−
|[http://git-scm.com/ git]
+
|[http://www.htslib.org/ BCFtools]
−
|2.9.5-IGB-gcc-4.9.4
+
|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
−
|Git is a free and open source distributed version control system designedto handle everything from small to very large projects with speed and efficiency.
+
|BCFtools is a set of utilities that manipulate variant calls in the  Variant Call Format (VCF) and its binary counterpart BCF
 
|-
 
|-
−
|[https://github.com/LangilleLab/microbiome_helper microbiome_helper]
+
|[https://github.com/arq5x/bedtools2 BEDTools]
−
|20171114-IGB-gcc-4.9.4
+
|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
−
|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.
+
|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/Illumina/strelka strelka]
+
|[https://github.com/PacificBiosciences/blasr BLASR]
−
|2.9.9
+
|4.0.0-IGB-gcc-4.9.4
−
|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.  
+
|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://github.com/PacificBiosciences/ccs pbccs]
+
|[http://blast.ncbi.nlm.nih.gov/ BLAST]
−
|4.0
+
|2.2.26-Linux_x86_64
−
|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.
+
|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://github.com/najoshi/sabre sabre]
+
|[http://blast.ncbi.nlm.nih.gov/ BLAST+]
−
|20171114-IGB-gcc-4.9.4
+
|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
−
|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.
+
|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://ccb.jhu.edu/software/stringtie/gffcompare.shtml gffcompare]
+
|[http://genome.ucsc.edu/FAQ/FAQblat.html BLAT]
−
|0.10.6-IGB-gcc-4.9.4
+
|3.5-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).  
+
|BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
 
|-
 
|-
−
|[http://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2]
+
|[https://github.com/Gaius-Augustus/BRAKER BRAKER]
−
|2.1-IGB-gcc-4.9.4
+
|2.1.2-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/
+
|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.
 
|-
 
|-
−
|expat
+
|[https://github.com/BSSeeker/BSseeker2 BS-Seeker]
−
|
+
|2.1.2-IGB-gcc-4.9.4-Python-2.7.13
−
|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)
+
|BS Seeker 2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated short reads.
 
|-
 
|-
−
|[http://cole-trapnell-lab.github.io/cufflinks/ Cufflinks]
+
|[https://github.com/hellbelly/BS-Snper BS-Snper]
−
|2.2.1<br>2.2.1-IGB-gcc-4.9.4-b4fa050
+
|20170222-IGB-gcc-4.9.4-Perl-5.24.1
−
|Transcript assembly, differential expression, and differential regulation for RNA-Seq
+
|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://cunit.sourceforge.net/ CUnit]
+
|[http://busco.ezlab.org/ BUSCO]
−
|2.1-3-IGB-gcc-4.9.4
+
|3.0.1-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|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.
 
|-
 
|-
−
|[https://github.com/mgbellemare/Arcade-Learning-Environment ArcadeLearningEnvironment]
+
|[http://bio-bwa.sourceforge.net/ BWA]
−
|0.5.1-IGB-gcc-4.9.4-Python-2.7.13
+
|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
−
|The Arcade Learning Environment (ALE) -- a platform for AI research. - Homepage: https://github.com/mgbellemare/Arcade-Learning-Environment
+
|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/lebedov/scikit-cuda scikit-cuda]
+
|[https://github.com/soedinglab/BaMMmotif2 BaMMmotif]
−
|0.5.1-IGB-gcc-4.9.4-Python-2.7.13
+
|2.0
−
|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.
+
|Bayesian Markov Model motif discovery software (version 2).
 
|-
 
|-
−
|[http://www.jalview.org/ Jalview]
+
|[https://github.com/pezmaster31/bamtools BamTools]
−
|2.11.0-Java-1.8.0_152
+
|2.4.1-IGB-gcc-4.9.4<br>2.5.1-IGB-gcc-4.9.4
−
|
+
|BamTools provides both a programmers API and an end-users toolkit for handling BAM files.
 
|-
 
|-
−
|[http://opencv.org/ OpenCV]
+
|[https://git.wageningenur.nl/medema-group/BiG-SCAPE BiG-SCAPE]
−
|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
+
|20181115-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|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)
 
|-
 
|-
−
|[https://github.com/bbuchfink/diamond DIAMOND]
+
|[http://www.bioperl.org/ BioPerl]
−
|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>0.9.9-IGB-gcc-4.9.4
+
|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
−
|Accelerated BLAST compatible local sequence aligner
+
|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.
 
|-
 
|-
−
|[http://liulab.dfci.harvard.edu/MACS/ MACS]
+
|[https://github.com/maasha/biopieces Biopieces]
−
|1.4.2-1-IGB-gcc-4.9.4-Python-2.7.13
+
|2.0-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.
+
|Biopieces is a bioinformatic framework of tools easily used and easily created.
 
|-
 
|-
−
|[http://nodejs.org nodejs]
+
|[http://www.biopython.org Biopython]
−
|10.16.2-IGB-gcc-4.9.4<br>9.9.0-IGB-gcc-4.9.4
+
|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-8.2.0-Python-3.7.2
−
|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.
+
|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.  
 
|-
 
|-
−
|[https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger spaceranger]
+
|[http://www.bioinformatics.babraham.ac.uk/projects/bismark/ Bismark]
−
|1.0.0
+
|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
−
|Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield 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.
+
|A tool to map bisulfite converted sequence reads and determine cytosine methylation states
 
|-
 
|-
−
|LibTIFF
+
|Bison
 
|
 
|
−
|tiff: Library and tools for reading and writing TIFF data files
+
|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://download.rsat.eu/ RSAT]
+
|Boost
−
|2018-08-04-IGB-gcc-4.9.4
+
|
−
|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
+
|Boost provides free peer-reviewed portable C++ source libraries.
 
|-
 
|-
−
|[https://github.com/HAugustijn/BiG-MAP2 big-map2-process]
+
|[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
−
|20200124
+
|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
−
|This is the Github repository for the Biosynthetic Gene cluster Meta’omics abundance Profiler
+
|Bowtie is an ultrafast, memory-efficient short read aligner.It aligns short DNA sequences (reads) to the human genome.
 
|-
 
|-
−
|[https://developer.nvidia.com/cudnn cuDNN]
+
|[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]
−
|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-IGB-gcc-4.9.4-CUDA-9.0.176<br>7.1.4-IGB-gcc-4.9.4-CUDA-9.0.176<br>7.6.1.34-CUDA-10.0.130
+
|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
−
|The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for    deep neural networks.
+
|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://git-lfs.github.com/ git-lfs]
+
|[http://bioinform.github.io/breakseq2/ BreakSeq2]
−
|2.2.1-IGB-gcc-4.9.4
+
|2.2-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|Ultrafast and accurate nucleotide-resolution analysis of structural variants - Homepage: http://bioinform.github.io/breakseq2/
 
|-
 
|-
−
|[http://snver.sourceforge.net/ SNVer]
+
|[http://weizhong-lab.ucsd.edu/cd-hit/ CD-HIT]
−
|0.5.3-Java-1.8.0_121<br>0.5.3-Java-1.8.0_152
+
|4.6.6-IGB-gcc-4.9.4
−
|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.
+
|CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. - Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
 
|-
 
|-
−
|[https://github.com/fidelram/deepTools deepTools]
+
|CMake
−
|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
 
−
|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.
 
−
|-
 
−
|libdrm
 
 
|
 
|
−
|Direct Rendering Manager runtime library.
+
|CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
 
|-
 
|-
−
|[http://www.novocraft.com/ novocraft]
+
|[https://github.com/abyzovlab/CNVnator CNVnator]
−
|3.08.00
+
|0.3.3-IGB-gcc-4.9.4
−
|Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms.
+
|a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
 
|-
 
|-
−
|h5py
+
|[https://github.com/BinPro/CONCOCT CONCOCT]
−
|
+
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
−
|The h5py package provides both a high- and low-level interface to the HDF5 library from Python.
+
|A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
 
|-
 
|-
−
|[http://www-inf.enst.fr/~demaille/a2ps/ a2ps]
+
|[https://developer.nvidia.com/cuda-toolkit CUDA]
−
|4.14-IGB-gcc-4.9.4
+
|10.0.130<br>8.0.61<br>8.0.61-IGB-gcc-4.9.4<br>9.0.176-IGB-gcc-4.9.4<br>9.1.85
−
|a2ps-4.14: Formats an ascii file for printing on a postscript printer
+
|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.
 
|-
 
|-
−
|GMP
+
|[http://cunit.sourceforge.net/ CUnit]
−
|
+
|2.1-3-IGB-gcc-4.9.4
−
|GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.  
+
|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.
 
|-
 
|-
−
|[https://github.com/GregoryFaust/samblaster samblaster]
+
|[https://github.com/marbl/canu Canu]
−
|0.1.24-IGB-gcc-4.9.4
+
|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
−
|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.
+
|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).
 
|-
 
|-
−
|[https://microbiology.se/software/itsx/ ITSx]
+
|[http://ecogenomics.github.io/CheckM CheckM]
−
|1.1.1-IGB-gcc-4.9.4
+
|1.0.7-IGB-gcc-4.9.4-Python-2.7.13
−
|TSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
+
|CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
 
|-
 
|-
−
|[http://www.perl.org/ Perl]
+
|[http://sanger-pathogens.github.io/circlator/ Circlator]
−
|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
+
|1.5.1-IGB-gcc-4.9.4-Python-3.6.1
−
|Larry Wall Practical Extraction and Report Language
+
|A tool to circularize genome assemblies.
 
|-
 
|-
−
|[https://xiph.org/flac/ FLAC]
+
|[http://www.circos.ca/ Circos]
−
|1.3.1-IGB-gcc-4.9.4
+
|0.69-4-IGB-gcc-4.9.4-Perl-5.24.1
−
|Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.
+
|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. - Homepage: http://www.circos.ca/
 
|-
 
|-
−
|Miniconda3
+
|Clp
 
|
 
|
−
|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.
+
|Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.  
 
|-
 
|-
−
|[http://genomethreader.org/ GenomeThreader]
+
|[http://www.clustal.org/omega/ Clustal-Omega]
−
|1.7.1
+
|1.2.4-IGB-gcc-4.9.4
−
|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.
+
|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  - Homepage: http://www.clustal.org/omega/
 
|-
 
|-
−
|gengetopt
+
|[http://www.ebi.ac.uk/Tools/msa/clustalw2/ ClustalW2]
−
|
+
|2.1-IGB-gcc-4.9.4
−
|Gengetopt is a tool to write command line option parsing code for C programs. - Homepage: https://www.gnu.org/software/gengetopt/gengetopt.html
+
|ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. - Homepage: http://www.ebi.ac.uk/Tools/msa/clustalw2/
 
|-
 
|-
−
|[http://www.netlab.uky.edu/p/bioinfo/MapSplice2 MapSplice]
+
|[https://github.com/PacificBiosciences/ConsensusCore ConsensusCore]
−
|2.2.1-IGB-gcc-4.9.4-Python-2.7.13
+
|1.0.1-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.
+
|ConsensusCore is a library of C++ algorithms for PacBio multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET).
 
|-
 
|-
−
|[http://rnaseq-mats.sourceforge.net/ rMATS]
+
|[http://cole-trapnell-lab.github.io/cufflinks/ Cufflinks]
−
|3.2.5-IGB-gcc-4.9.4-Python-2.7.13
+
|2.2.1<br>2.2.1-IGB-gcc-4.9.4-b4fa050
−
|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.
+
|Transcript assembly, differential expression, and differential regulation for RNA-Seq
 
|-
 
|-
−
|[https://github.com/csmiller/EMIRGE EMIRGE]
+
|[http://cython.org/ Cython]
−
|0.61.1-IGB-gcc-4.9.4-Python-2.7.13
+
|0.27.3-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.
+
|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.  
 
|-
 
|-
−
|[http://www.bork.embl.de/pal2nal/ pal2nal]
+
|[https://sites.google.com/site/danposdoc/news DANPOS]
−
|14-IGB-gcc-4.9.4
+
|2.2.2-IGB-gcc-4.9.4-Python-2.7.13-R-3.3.3
−
|PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment.
+
|A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2
 
|-
 
|-
−
|[https://vcftools.github.io VCFtools]
+
|[http://www.oracle.com/technetwork/products/berkeleydb DB]
−
|0.1.15-IGB-gcc-4.9.4-Perl-5.24.1
+
|18.1.32-IGB-gcc-4.9.4
−
|The aim of VCFtools is to provide  easily accessible methods for working with complex  genetic variation data in the form of VCF files. - Homepage: https://vcftools.github.io
+
|Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
 
|-
 
|-
−
|fontconfig
+
|[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>0.9.9-IGB-gcc-4.9.4
−
|Fontconfig is a library designed to provide system-wide font configuration, customization andapplication access.
+
|Accelerated BLAST compatible local sequence aligner
 
|-
 
|-
−
|OpenPGM
+
|[http://www.broadinstitute.org/software/discovar/blog/ DISCOVARdenovo]
−
|
+
|52488-IGB-gcc-4.9.4
−
|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.
+
|DISCOVAR de novo can generate de novo assemblies for both large and small genomes. It currently does not call variants.
 
|-
 
|-
−
|[http://eddylab.org/software.html squid]
+
|[http://www1.montpellier.inra.fr/CBGP/diyabc/index.php DIYABC]
−
|1.9g-IGB-gcc-4.9.4
+
|2.1.0
−
|A C library that is bundled with much of the above software. C function library for sequence analysis.
+
|a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers
 
|-
 
|-
−
|[https://github.com/hellbelly/BS-Snper BS-Snper]
+
|[https://dendropy.org/ DendroPy]
−
|20170222-IGB-gcc-4.9.4-Perl-5.24.1
+
|4.4.0-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|DendroPy is a Python library for phylogenetic computing.  
 
|-
 
|-
−
|Automake
+
|[http://www.doxygen.org Doxygen]
−
|
+
|1.8.13-IGB-gcc-4.9.4
−
|Automake: GNU Standards-compliant Makefile generator
+
|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.
 
|-
 
|-
−
|[https://github.com/LLNL/ior ior]
+
|[http://emboss.sourceforge.net/ EMBOSS]
−
|3.0.1-IGB-gcc-4.9.4
+
|6.6.0-IGB-gcc-4.9.4-Java-1.8.0_121
−
|Parallel filesystem I/O benchmark
+
|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.
 
|-
 
|-
−
|[http://www.nasm.us/ NASM]
+
|[https://github.com/csmiller/EMIRGE EMIRGE]
−
|2.12.02-IGB-gcc-4.9.4
+
|0.61.1-IGB-gcc-4.9.4-Python-2.7.13
−
|NASM: General-purpose x86 assembler
+
|EMIRGE reconstructs full length ribosomal genes from short readsequencing data.  In the process, it also provides estimates of thesequences abundances.
 
|-
 
|-
−
|[https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]
+
|[http://easybuilders.github.com/easybuild/ EasyBuild]
−
|2.0.5-IGB-gcc-4.9.4<br>2.1.0-IGB-gcc-4.9.4
+
|3.5.3<br>3.6.0<br>3.6.2<br>3.9.3
−
|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).
+
|EasyBuild is a software build and installation frameworkwritten in Python that allows you to install software in a structured,repeatable and robust way.
 
|-
 
|-
−
|[https://www.pmgenomics.ca/hoffmanlab/proj/segway/ Segway]
+
|Eigen
−
|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.
+
|Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
 
|-
 
|-
−
|[https://github.com/dmlc/xgboost xgboost]
+
|[http://pb-falcon.readthedocs.io/en/latest/index.html FALCON]
−
|0.80-IGB-gcc-4.9.4-Python-3.6.1
+
|1.8.8-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|FALCON is a diploid aware genome assembler designed for Pacific Biosciences long read data.
 
|-
 
|-
−
|[http://lowelab.ucsc.edu/snoscan/ snoscan]
+
|[https://github.com/PacificBiosciences/FALCON_unzip FALCON_unzip]
−
|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
+
|0.4.0-IGB-gcc-4.9.4-Python-2.7.13
−
|Search for C/D box methylation guide snoRNA genes in a genomic sequence
+
|FALCON-Unzip contains the modules that works with FALCON for full diploid assembly (representing haplotype specific contigs as "haplotigs" as assembly output).
 
|-
 
|-
−
|[https://github.com/IGBIllinois/VICSIN VICSIN]
+
|[http://hannonlab.cshl.edu/fastx_toolkit/ FASTX-Toolkit]
−
|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>dev
+
|0.0.14-IGB-gcc-4.9.4
−
|VICSIN = Viral, Integrative, and Conjugative Sequence Identification and Networking
+
|The FASTX-Toolkit is a collection of command line tools for  Short-Reads FASTA/FASTQ files preprocessing. - Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
 
|-
 
|-
−
|[http://wasabiapp.org/software/prank/ PRANK]
+
|[https://github.com/tderrien/FEELnc FEELnc]
−
|170427-IGB-gcc-4.9.4
+
|20180117-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.
+
|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).  
 
|-
 
|-
−
|[https://github.com/lisa-lab/pylearn2 pylearn2]
+
|FFTW
−
|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
+
|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.
 
|-
 
|-
−
|[https://github.com/Gaius-Augustus/BRAKER BRAKER]
+
|[https://www.ffmpeg.org/ FFmpeg]
−
|2.1.2-IGB-gcc-4.9.4
+
|3.3-IGB-gcc-4.9.4
−
|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.
+
|A complete, cross-platform solution to record, convert and stream audio and video. - Homepage: https://www.ffmpeg.org/
 
|-
 
|-
−
|[http://eddylab.org/infernal/ Infernal]
+
|[https://xiph.org/flac/ FLAC]
−
|1.1.2-IGB-gcc-4.9.4
+
|1.3.1-IGB-gcc-4.9.4
−
|Infernal,INFERence of RNA ALignment, is for searching DNA sequence databases for RNA structure and sequence similarities.
+
|Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.
 
|-
 
|-
−
|[http://ocaml.org/ OCaml]
+
|[https://github.com/dstreett/FLASH2 FLASH2]
−
|4.05.0-IGB-gcc-4.9.4
+
|2.2.00-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.
+
|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.
 
|-
 
|-
−
|[https://github.com/google/googletest gtest]
+
|[https://github.com/md5sam/Falcon2Fastg Falcon2Fastg]
−
|1.8.0-IGB-gcc-4.9.4
+
|0.3.1-IGB-gcc-4.9.4-Python-2.7.13
−
|Googles C++ test framework
+
|This software converts the results of PacBio assembly using FALCON, to a FASTG graph that can be visualized using Bandage.
 
|-
 
|-
−
|[https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger cellranger]
+
|[http://www.atgc-montpellier.fr/fastme/binaries.php FastME]
−
|2.1.0<br>2.1.1<br>3.0.0<br>3.0.1<br>3.1.0
+
|2.1.6.1-IGB-gcc-4.9.4
−
|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.
+
|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://www.cbcb.umd.edu/software/glimmer/ GLIMMER]
+
|[http://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FastQC]
−
|3.02b-IGB-gcc-4.9.4
+
|0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152<br>0.11.8-IGB-gcc-4.9.4-Java-1.8.0_152<br>0.11.8-Java-1.8.0_152
−
|Glimmer is a system for finding genes in microbial DNA, especiallythe genomes of bacteria, archaea, and viruses.
+
|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://ant.apache.org/ ant]
+
|[http://www.microbesonline.org/fasttree/ FastTree]
−
|1.10.1-Java-1.8.0_121<br>1.10.1-Java-1.8.0_152
+
|2.1.10-IGB-gcc-4.9.4
−
|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.
+
|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.  
 
|-
 
|-
−
|libgtextutils
+
|[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
−
|ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream - Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
+
|Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
 
|-
 
|-
−
|[https://github.com/CGATOxford/UMI-tools umi-tools]
+
|[https://github.com/ekg/freebayes FreeBayes]
−
|1.0.1-IGB-gcc-8.2.0-Python-3.7.2
+
|1.1.0-IGB-gcc-4.9.4
−
|Tools for handling Unique Molecular Identifiers in NGS data sets
+
|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.
 
|-
 
|-
−
|efiest/beta
+
|[https://www.gams.com/ GAMS]
−
|beta
+
|23.6.5
−
|
+
|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/davidemms/OrthoFinder OrthoFinder]
+
|[http://www.broadinstitute.org/gatk/ GATK]
−
|2.2.7<br>2.3.7-IGB-gcc-4.9.4
+
|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
−
|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.  
+
|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.
 
|-
 
|-
−
|[http://www.htslib.org/ HTSlib]
+
|[https://github.com/halelab/GBS-SNP-CROP GBS-SNP-CROP]
−
|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
+
|4.0-IGB-gcc-4.9.4
−
|A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
+
|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.
 
|-
 
|-
−
|[https://github.com/pjeraldo/imtornado2 IM-TORNADO]
+
|GCC
−
|2.0.3.3-IGB-gcc-4.9.4-Python-2.7.13
+
|
−
|A pipeline for 16S reads from paired-end libraries
+
|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.crypticlineage.net/pages/distruct.html distruct]
+
|GCCcore
−
|2.2-IGB-gcc-4.9.4
+
|
−
|Modified version of the original distruct.py
+
|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,...).
 
|-
 
|-
−
|[https://github.com/nanoporetech/scrappie scrappie]
+
|[http://search.cpan.org/~lds/GD/ GD]
−
|1.3.0-IGB-gcc-4.9.4
+
|2.66-IGB-gcc-4.9.4-Perl-5.24.1
−
|Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group.
+
|GD.pm - Interface to Gd Graphics Library
 
|-
 
|-
−
|[https://github.com/COMBINE-lab/SalmonTools SalmonTools]
+
|[http://www.gdal.org/ GDAL]
−
|20190604-IGB-gcc-8.2.0
+
|2.3.1-IGB-gcc-4.9.4<br>3.0.3-IGB-gcc-8.2.0
−
|Useful tools for working with Salmon output
+
|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://qiime.org/ QIIME2]
+
|GEOS
−
|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
+
|
−
|QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
+
|GEOS (Geometry Engine - Open Source) is a C++ port of the  Java Topology Suite (JTS)
 
|-
 
|-
−
|[https://www.continuum.io/anaconda-overview Anaconda2]
+
|[https://bitbucket.org/feeldead/gfold GFOLD]
−
|4.3.1
+
|1.1.4-IGB-gcc-4.9.4
−
|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
+
|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.
 
|-
 
|-
−
|ScaLAPACK
+
|[http://www.cbcb.umd.edu/software/glimmer/ GLIMMER]
−
|
+
|3.02b-IGB-gcc-4.9.4
−
|The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
+
|Glimmer is a system for finding genes in microbial DNA, especiallythe genomes of bacteria, archaea, and viruses.
 
|-
 
|-
−
|[http://biom-format.org/ biom-format]
+
|[http://www.gtk.org/ GLib]
−
|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
+
|2.62.3-IGB-gcc-4.9.4
−
|The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables.
+
|GLib is one of the base libraries of the GTK+ project
 
|-
 
|-
−
|[https://melodi.ee.washington.edu/gmtk/ GMTK]
+
|[http://research-pub.gene.com/gmap/ GMAP]
−
|1.4.4-IGB-gcc-4.9.4
+
|2018-05-30-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.
+
|A Genomic Mapping and Alignment Program for mRNA and EST Sequences, andGSNAP: Genomic Short-read Nucleotide Alignment Program
 
|-
 
|-
−
|[https://github.com/lh3/minimap minimap]
+
|[http://research-pub.gene.com/gmap/ GMAP-GSNAP]
−
|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>2.3-IGB-gcc-4.9.4<br>2.8-IGB-gcc-4.9.4
+
|2017-11-15-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.  
+
|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.  
 
|-
 
|-
−
|[https://github.com/tderrien/FEELnc FEELnc]
+
|[https://melodi.ee.washington.edu/gmtk/ GMTK]
−
|20180117-IGB-gcc-4.9.4
+
|1.4.4-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).  
+
|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.
 
|-
 
|-
−
|libxslt
+
|GObject-Introspection
 
|
 
|
−
|Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
+
|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.
 
|-
 
|-
−
|[https://github.com/ComparativeGenomicsToolkit/cactus cactus]
+
|GSL
−
|20180705-IGB-gcc-4.9.4-Python-2.7.13
+
|
−
|Cactus is a reference-free whole-genome multiple alignment program.
+
|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://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate exonerate]
+
|[https://developer.gnome.org/gtk+/stable/ GTK+]
−
|2.2.0-IGB-gcc-4.9.4
+
|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
−
|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.
+
|The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
 
|-
 
|-
−
|[https://github.com/PacificBiosciences/blasr BLASR]
+
|[http://guidance.tau.ac.il/ver2/ GUIDANCE]
−
|4.0.0-IGB-gcc-4.9.4
+
|2.02-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.  
+
|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/
 
|-
 
|-
−
|[http://invisible-island.net/byacc/byacc.html byacc]
+
|Gdk-Pixbuf
−
|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.
 
−
|-
 
−
|VarScan
 
−
|2.3.9-Java-1.8.0_152
 
 
|
 
|
 +
|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.
 
|-
 
|-
−
|libgdiplus
+
|[http://exon.gatech.edu/GeneMark/ GeneMark-ES]
−
|
+
|4.33-IGB-gcc-4.9.4-Perl-5.24.1<br>4.33-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
−
|An Open Source implementation of the GDI+ API
+
|Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training.
 
|-
 
|-
−
|[https://github.com/Discngine/fpocket fpocket]
+
|[http://exon.gatech.edu/GeneMark/ GeneMarkS]
−
|3.1.3-IGB-gcc-4.9.4
+
|4.30-IGB-gcc-4.9.4
−
|fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.
+
|GeneMarkS: a self-training method for prediction of gene starts in microbial genomes
 
|-
 
|-
−
|[http://expressionanalysis.github.io/ea-utils/ ea-utils]
+
|[http://genomethreader.org/ GenomeThreader]
−
|1.04.807-IGB-gcc-4.9.4
+
|1.7.1
−
|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.
+
|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://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger longranger]
+
|[https://github.com/PacificBiosciences/GenomicConsensus GenomicConsensus]
−
|2.1.3<br>2.1.6<br>2.2.2
+
|3.0.2-IGB-gcc-4.9.4-Python-2.7.13
−
|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
+
|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.
 
|-
 
|-
−
|[http://multiqc.info/ MultiQC]
+
|[http://ghostscript.com GhostScript]
−
|0.9-IGB-gcc-4.9.4-Python-2.7.13<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
+
|9.21-IGB-gcc-4.9.4
−
|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.
+
|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. - Homepage: http://ghostscript.com
 
|-
 
|-
−
|[https://github.com/gjospin/PhyloSift PhyloSift]
+
|[https://ccb.jhu.edu/software/glimmerhmm GlimmerHMM]
−
|1.0.0_01-IGB-gcc-4.9.4-Perl-5.24.1
+
|3.0.4-IGB-gcc-4.9.4
−
|PhyloSift is a suite of software tools to conduct phylogeneticanalysis of genomes and metagenomes.
+
|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.
 
|-
 
|-
−
|[http://broadinstitute.github.io/picard/ picard]
+
|[https://gradle.org Gradle]
−
|2.10.1-Java-1.8.0_121<br>2.10.1-Java-1.8.0_152<br>2.9.0-Java-1.8.0_121<br>2.9.4-Java-1.8.0_121
+
|4.7
−
|A set of tools (in Java) for working with next generation sequencing data in the BAM  (http://samtools.github.io/hts-specs) format.
+
|Complete Gradle install.From mobile apps to microservices, from small startups to big enterprises,Gradle helps teams build, automate and deliver better software, faster.  
 
|-
 
|-
−
|[http://mummer.sourceforge.net/ MUMmer]
+
|[http://www.graphicsmagick.org/ GraphicsMagick]
−
|3.23-IGB-gcc-4.9.4<br>4.0.0beta2-IGB-gcc-4.9.4
+
|1.3.26-IGB-gcc-4.9.4
−
|MUMmer is a system for rapidly aligning entire genomes
+
|GraphicsMagick is the swiss army knife of image processing.
 
|-
 
|-
−
|[https://github.com/laurikari/tre tre]
+
|[https://sourceforge.net/projects/biogrinder/ Grinder]
−
|20161208-IGB-gcc-4.9.4
+
|0.5.4-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.
+
|Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
 
|-
 
|-
−
|libpthread-stubs
+
|[http://www.gurobi.com/ Gurobi]
−
|
+
|7.5.2
−
|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.
+
|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.
 
|-
 
|-
−
|[http://deweylab.github.io/RSEM/ RSEM]
+
|[http://www.hdfgroup.org/HDF5/ HDF5]
−
|1.3.0-IGB-gcc-4.9.4<br>1.3.1-IGB-gcc-4.9.4
+
|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
−
|RNA-Seq by Expectation-Maximization
+
|HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
 
|-
 
|-
−
|[https://community.nanoporetech.com/posts/pre-release-of-stand-alone guppy-gpu]
+
|[https://ccb.jhu.edu/software/hisat2/index.shtml HISAT2]
−
|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>3.4.5
+
|2.0.5-IGB-gcc-4.9.4<br>2.1.0-IGB-gcc-4.9.4
−
|Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.  
+
|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://pillow.readthedocs.org/ Pillow]
+
|[http://hmmer.org/ HMMER]
−
|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
+
|2.3.2-IGB-gcc-4.9.4<br>3.1b2-IGB-gcc-4.9.4<br>3.2.1-IGB-gcc-4.9.4
−
|Pillow is the friendly PIL fork by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
+
|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.
 
|-
 
|-
−
|[https://t3f.readthedocs.io/en/latest/index.html t3f]
+
|[http://homer.ucsd.edu/homer/ HOMER]
−
|1.1.0-IGB-gcc-4.9.4-Python-3.6.1
+
|4.9.1-IGB-gcc-4.9.4-Perl-5.24.1
−
|t3f is a library for working with Tensor Train decomposition.  
+
|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://pygraphviz.github.io/ pygraphviz]
+
|[https://github.com/rhuebler/HOPS HOPS]
−
|1.3.1-IGB-gcc-4.9.4-Python-3.6.1
+
|0.33
−
|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.
+
|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.
 +
|-
 +
|[http://www-huber.embl.de/users/anders/HTSeq/ HTSeq]
 +
|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
 +
|A framework to process and analyze data from high-throughput sequencing (HTS) assays
 +
|-
 +
|[http://www.htslib.org/ HTSlib]
 +
|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
 +
|A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
 +
|-
 +
|[http://huttenhower.sph.harvard.edu/humann2 HUMAnN2]
 +
|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
 +
|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).
 +
|-
 +
|HarfBuzz
 +
|
 +
|HarfBuzz is an OpenType text shaping engine. - Homepage: http://www.freedesktop.org/wiki/Software/HarfBuzz
 +
|-
 +
|[https://github.com/nservant/HiC-Pro HiC-Pro]
 +
|2.9.0-IGB-gcc-4.9.4-Python-2.7.13
 +
|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://github.com/kundajelab/idr IDR]
 
|[https://github.com/kundajelab/idr IDR]
Line 481: Line 505:
 
|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).
 
|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://www.ruby-lang.org Ruby]
+
|IGB-gcc
−
|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.
+
|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
 
|-
 
|-
−
|[https://github.com/martinwu/AMPHORA2 AMPHORA2]
+
|[https://github.com/pjeraldo/imtornado2 IM-TORNADO]
−
|20190104-IGB-gcc-4.9.4
+
|2.0.3.3-IGB-gcc-4.9.4-Python-2.7.13
−
|An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
+
|A pipeline for 16S reads from paired-end libraries
 
|-
 
|-
−
|[http://www.yandell-lab.org/software/maker.html MAKER]
+
|[http://ipython.org/index.html IPython]
−
|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>3.01.1-beta-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
+
|5.3.0-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|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.
 
|-
 
|-
−
|[https://github.com/DpeerLab/magic magic]
+
|[https://microbiology.se/software/itsx/ ITSx]
−
|0.1-IGB-gcc-4.9.4-Python-3.6.1<br>0.1.1-IGB-gcc-4.9.4-Python-3.6.1
+
|1.1.1-IGB-gcc-4.9.4
−
|A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data
+
|TSx: Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for use in environmental sequencing
 
|-
 
|-
−
|[http://www.mpich.org/ MPICH]
+
|[https://databank.illinois.edu/ IllinoisDataBank]
−
|3.0.4-GCC-4.9.4-2.28
+
|1.0-IGB-gcc-4.9.4-Python-3.6.1
−
|MPICH v3.x is an open source high-performance MPI 3.0 implementation.It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
+
|The Illinois Data Bank is a public access repository for publishing research data from the University of Illinois at Urbana-Champaign
 
|-
 
|-
−
|[http://www.repeatmasker.org/RMBlast.html RMBlast]
+
|[http://www.imagemagick.org/ ImageMagick]
−
|2.6.0-IGB-gcc-4.9.4
+
|7.0.5-5-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.
+
|ImageMagick is a software suite to create, edit, compose, or convert bitmap images - Homepage: http://www.imagemagick.org/
 
|-
 
|-
−
|GEOS
+
|[http://eddylab.org/infernal/ Infernal]
−
|
+
|1.1.2-IGB-gcc-4.9.4
−
|GEOS (Geometry Engine - Open Source) is a C++ port of the  Java Topology Suite (JTS)
+
|Infernal,INFERence of RNA ALignment, is for searching DNA sequence databases for RNA structure and sequence similarities.
 
|-
 
|-
−
|[https://www.continuum.io/anaconda-overview Anaconda3]
+
|[https://www.ebi.ac.uk/interpro/interproscan.html InterProScan]
−
|2019.10<br>5.0.1<br>5.1.0
+
|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
−
|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.
+
|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.
 
|-
 
|-
−
|efiest/prod
+
|JUnit
−
|prod
 
 
|
 
|
 +
|A programmer-oriented testing framework for Java.
 
|-
 
|-
−
|[http://www.lua.org/ Lua]
+
|[http://www.jalview.org/ Jalview]
−
|5.1.5-IGB-gcc-4.9.4<br>5.3.4-IGB-gcc-4.9.4
+
|2.11.0-Java-1.8.0_152
−
|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.
+
|
 
|-
 
|-
−
|[http://ecogenomics.github.io/CheckM CheckM]
+
|[http://www.ece.uvic.ca/~frodo/jasper/ JasPer]
−
|1.0.7-IGB-gcc-4.9.4-Python-2.7.13
+
|1.900.1-IGB-gcc-4.9.4<br>2.0.10-IGB-gcc-4.9.4
−
|CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
+
|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. - Homepage: http://www.ece.uvic.ca/~frodo/jasper/
 
|-
 
|-
−
|[https://faculty.washington.edu/browning/beagle/beagle.html beagle]
+
|[http://java.com/ Java]
−
|03Jul18.40b-Java-1.8.0_152
+
|1.8.0_121<br>1.8.0_152<br>1.8.0_201<br>11.0.5
−
|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.  
+
|Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
 
|-
 
|-
−
|[http://www.unidata.ucar.edu/software/netcdf/ netCDF]
+
|[http://www.genome.umd.edu/jellyfish.html Jellyfish]
−
|4.4.1.1-IGB-gcc-4.9.4<br>4.7.2-IGB-gcc-8.2.0
+
|1.1.12-IGB-gcc-4.9.4<br>2.2.10-IGB-gcc-8.2.0<br>2.2.6-IGB-gcc-4.9.4
−
|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.
+
|Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
 
|-
 
|-
−
|[https://databank.illinois.edu/ IllinoisDataBank]
+
|[https://github.com/aidenlab/juicer Juicer]
−
|1.0-IGB-gcc-4.9.4-Python-3.6.1
+
|1.13.02-Java-1.8.0_152
−
|The Illinois Data Bank is a public access repository for publishing research data from the University of Illinois at Urbana-Champaign
+
|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.
 
|-
 
|-
−
|[http://numba.pydata.org/ numba]
+
|[https://github.com/TGAC/KAT KAT]
−
|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
+
|2.4.1-IGB-gcc-4.9.4
−
|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.
+
|KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts.  
 
|-
 
|-
−
|[https://web.stanford.edu/group/pritchardlab/structure.html structure]
+
|[https://github.com/fchollet/keras Keras]
−
|2.3.4-IGB-gcc-4.9.4
+
|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>2.2.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.2.4-IGB-gcc-4.9.4-Python-3.6.1
−
|The program structure is a free software package for using multi-locus genotype data to investigate population structure.
+
|Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.  
 
|-
 
|-
−
|binutils
+
|[https://bitbucket.org/biobakery/kneaddata/wiki/Home KneadData]
−
|
+
|0.6.1-IGB-gcc-4.9.4-Python-3.6.1
−
|binutils: GNU binary utilities
+
|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://rclone.org/ rclone]
+
|[https://ccb.jhu.edu/software/kraken/ Kraken]
−
|1.41
+
|1.0-IGB-gcc-4.9.4
−
|Rclone is a command line program to sync files and directories to and from different cloud storage
+
|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/PacificBiosciences/FALCON_unzip FALCON_unzip]
+
|[https://ccb.jhu.edu/software/kraken/ Kraken2]
−
|0.4.0-IGB-gcc-4.9.4-Python-2.7.13
+
|2.0.8-beta-IGB-gcc-4.9.4
−
|FALCON-Unzip contains the modules that works with FALCON for full diploid assembly (representing haplotype specific contigs as "haplotigs" as assembly output).
+
|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.  
 
|-
 
|-
−
|[http://swift-lang.org/Swift-T/ swift-t]
+
|[https://github.com/marbl/Krona Krona]
−
|1.3-IGB-gcc-4.9.4
+
|2.7-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.  
+
|Interactively explore metagenomes and more from a web browser.
 
|-
 
|-
−
|[https://github.com/PacificBiosciences/pbbam pbbam]
+
|[http://lame.sourceforge.net/ LAME]
−
|1.0.7-IGB-gcc-8.2.0
+
|3.99.5-IGB-gcc-4.9.4
−
|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.
+
|LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
 
|-
 
|-
−
|[https://cran.r-project.org/web/packages/RcppGSL/index.html RcppGSL]
+
|[http://www.bx.psu.edu/~rsharris/lastz/ LASTZ]
−
|0.3.2-IGB-gcc-4.9.4-R-3.3.3
+
|1.04.00-IGB-gcc-4.9.4
−
|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.
+
|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/
 
|-
 
|-
−
|GObject-Introspection
+
|[https://bitbucket.org/nsegata/lefse LEfSe]
−
|
+
|20180219-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|LEfSe
 
|-
 
|-
−
|[http://deeplearning.net/software/libgpuarray pygpu]
+
|[http://www.bcgsc.ca/platform/bioinfo/software/links LINKS]
−
|0.6.5-IGB-gcc-4.9.4-Python-2.7.13
+
|1.8.5-IGB-gcc-4.9.4-Perl-5.24.1
−
|Python bindings for libgpuarray - Homepage: http://deeplearning.net/software/libgpuarray
+
|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).
 
|-
 
|-
−
|[https://github.com/marbl/MashMap MashMap]
+
|[http://llvm.org/ LLVM]
−
|2.0
+
|4.0.1-IGB-gcc-4.9.4<br>6.0.0-IGB-gcc-4.9.4
−
|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).
+
|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.
 +
|-
 +
|[https://symas.com/lmdb 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.
 +
|-
 +
|[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
 
|-
 
|-
−
|IGB-gcc
+
|LibTIFF
 
|
 
|
−
|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
+
|tiff: Library and tools for reading and writing TIFF data files
 
|-
 
|-
−
|[https://github.com/nservant/HiC-Pro HiC-Pro]
+
|[http://sourceforge.net/projects/libuuid/ LibUUID]
−
|2.9.0-IGB-gcc-4.9.4-Python-2.7.13
+
|1.0.3-IGB-gcc-4.9.4
−
|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.
+
|Portable uuid C library
 
|-
 
|-
−
|[https://mathema.tician.de/software/pycuda/ PyCUDA]
+
|[http://www.littlecms.com/ LittleCMS]
−
|2017.1-IGB-gcc-4.9.4-Python-2.7.13
+
|2.8-IGB-gcc-4.9.4
−
|PyCUDA lets you access Nvidia‘s CUDA parallel computation API from Python. - Homepage: https://mathema.tician.de/software/pycuda/
+
|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://libharu.org/ libharu]
+
|[http://www.lua.org/ Lua]
−
|2.3.0-IGB-gcc-4.9.4
+
|5.1.5-IGB-gcc-4.9.4<br>5.3.4-IGB-gcc-4.9.4
−
|libHaru is a free, cross platform, open source library for generating PDF files. - Homepage: http://libharu.org/
+
|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/lilydjwg/pssh pssh]
+
|M4
−
|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.
+
|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://www.circos.ca/ Circos]
+
|[http://liulab.dfci.harvard.edu/MACS/ MACS]
−
|0.69-4-IGB-gcc-4.9.4-Perl-5.24.1
+
|1.4.2-1-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. - Homepage: http://www.circos.ca/
+
|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.
 
|-
 
|-
−
|gompi
+
|[https://github.com/taoliu/MACS/ MACS2]
−
|
+
|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
−
|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
+
|Model Based Analysis for ChIP-Seq data
 
|-
 
|-
−
|[https://github.com/alexdobin/STAR STAR]
+
|[http://mafft.cbrc.jp/alignment/software/ MAFFT]
−
|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>2.7.3a-IGB-gcc-8.2.0
+
|7.310-IGB-gcc-4.9.4
−
|STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
+
|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. - Homepage: http://mafft.cbrc.jp/alignment/software/
 
|-
 
|-
−
|efiest/beta_private
+
|[http://www.yandell-lab.org/software/maker.html MAKER]
−
|beta_private
+
|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>3.01.1-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.zeromq.org/bindings:python PyZMQ]
+
|[https://github.com/LynchLab/MAPGD MAPGD]
−
|16.0.2-IGB-gcc-4.9.4-Python-3.6.1
+
|0.4.26-IGB-gcc-4.9.4
−
|Python bindings for ZeroMQ
+
|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.
 
|-
 
|-
−
|[https://cran.r-project.org/web/packages/h2o/index.html h2o]
+
|[http://www.mathworks.com/products/matlab MATLAB]
−
|3.14.0.3-IGB-gcc-4.9.4-R-3.3.3
+
|2017a<br>2017b
−
|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.
+
|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://www.oracle.com/technetwork/products/berkeleydb DB]
+
|[https://www.mathworks.com/help/matlab/matlab-engine-for-python.html MATLAB-python]
−
|18.1.32-IGB-gcc-4.9.4
+
|2017b-IGB-gcc-4.9.4-Python-3.6.1
−
|Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
+
|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.
 
|-
 
|-
−
|[https://github.com/shawnzhangyx/PePr PePr]
+
|[http://micans.org/mcl/ MCL]
−
|1.1.21-IGB-gcc-4.9.4-Python-2.7.13
+
|14.137-IGB-gcc-4.9.4
−
|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.
+
|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.  - Homepage: http://micans.org/mcl/
 
|-
 
|-
−
|[http://matsen.fhcrc.org/pplacer/ pplacer]
+
|[https://github.com/voutcn/megahit MEGAHIT]
−
|1.1.alpha19
+
|1.1.1-IGB-gcc-4.9.4
−
|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.
+
|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. - Homepage: https://github.com/voutcn/megahit
 
|-
 
|-
−
|[http://orthomcl.org/ OrthoMCL]
+
|[http://ab.inf.uni-tuebingen.de/software/megan6/ MEGAN]
−
|2.0.9-IGB-gcc-4.9.4-Perl-5.24.1
+
|6.12.2-Java-1.8.0_152
−
|OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. - Homepage: http://orthomcl.org/
+
|MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.
 
|-
 
|-
−
|[http://lowelab.ucsc.edu/tRNAscan-SE/ tRNAscan-SE]
+
|[http://meme-suite.org/ MEME]
−
|1.3.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
+
|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
−
|tRNAscan-SE: a tool for finding transfer RNAs
+
|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.
 
|-
 
|-
−
|Boost
+
|[http://glaros.dtc.umn.edu/gkhome/metis/metis/overview METIS]
−
|
+
|5.1.0-IGB-gcc-4.9.4
−
|Boost provides free peer-reviewed portable C++ source libraries.
+
|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://www.makotemplates.org Mako]
+
|[https://github.com/soedinglab/MMseqs2 MMseqs2]
−
|1.0.6-IGB-gcc-4.9.4-Python-3.6.1
+
|10-6d92c
−
|A super-fast templating language that borrows the best ideas from the existing templating languages
+
|MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.  
 
|-
 
|-
−
|[http://www.canonware.com/jemalloc jemalloc]
+
|[http://www.mpich.org/ MPICH]
−
|5.0.1-IGB-gcc-4.9.4
+
|3.0.4-GCC-4.9.4-2.28
−
|jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
+
|MPICH v3.x is an open source high-performance MPI 3.0 implementation.It does not support InfiniBand (use MVAPICH2 with InfiniBand devices).
 
|-
 
|-
−
|[https://www.gnu.org/software/parallel/ parallel]
+
|[https://github.com/mitoNGS/MToolBox MToolBox]
−
|20170622-IGB-gcc-4.9.4
+
|1.0-IGB-gcc-4.9.4<br>1.2.1-IGB-gcc-4.9.4
−
|parallel: GNU parallel is a shell tool for executing jobs in parallel using one or more computers.  
+
|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.
 
|-
 
|-
−
|[http://huttenhower.sph.harvard.edu/humann2 HUMAnN2]
+
|[http://mummer.sourceforge.net/ MUMmer]
−
|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
+
|3.23-IGB-gcc-4.9.4<br>4.0.0beta2-IGB-gcc-4.9.4
−
|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).
+
|MUMmer is a system for rapidly aligning entire genomes
 
|-
 
|-
−
|[https://github.com/PacificBiosciences/ConsensusCore ConsensusCore]
+
|[http://drive5.com/muscle/ MUSCLE]
−
|1.0.1-IGB-gcc-4.9.4-Python-2.7.13
+
|3.8.31-IGB-gcc-4.9.4
−
|ConsensusCore is a library of C++ algorithms for PacBio multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET).
+
|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/
 
|-
 
|-
−
|glproto
+
|[http://www.genome.umd.edu/masurca.html MaSuRCA]
−
|
+
|3.2.3-IGB-gcc-4.9.4
−
|X protocol and ancillary headers
+
|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.broadinstitute.org/gatk/ GATK]
+
|[http://www.makotemplates.org Mako]
−
|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
+
|1.0.6-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|A super-fast templating language that borrows the best ideas from the existing templating languages
 
|-
 
|-
−
|[http://pytorch.org PyTorch]
+
|[http://www.netlab.uky.edu/p/bioinfo/MapSplice2 MapSplice]
−
|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
+
|2.2.1-IGB-gcc-4.9.4-Python-2.7.13
−
|Tensors and Dynamic neural networks in Pythonwith strong GPU acceleration.
+
|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://github.com/fenderglass/Flye Flye]
+
|[https://mariadb.org/ MariaDB]
−
|2.4.2-IGB-gcc-4.9.4-Python-2.7.13<br>2.7-IGB-gcc-4.9.4-Python-3.6.1
+
|10.1.31-IGB-gcc-4.9.4<br>10.1.31-IGB-gcc-8.2.0<br>5.5.58-IGB-gcc-4.9.4
−
|Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
+
|MariaDB An enhanced, drop-in replacement for MySQL.
 
|-
 
|-
−
|[https://ninja-build.org/ Ninja]
+
|[https://github.com/marbl/MashMap MashMap]
−
|1.9.0-IGB-gcc-4.9.4
+
|2.0
−
|Ninja is a small build system with a focus on speed.
+
|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/wdecoster/NanoPlot NanoPlot]
+
|[https://github.com/matterport/Mask_RCNN MaskRCNN]
−
|1.18.2-IGB-gcc-4.9.4-Python-3.6.1
+
|20190227-IGB-gcc-4.9.4-Python-3.6.1
−
|Plotting tool for long read sequencing data and alignments.
+
|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.  
 
|-
 
|-
−
|GSL
+
|[http://www.coxdocs.org/doku.php?id=maxquant:start MaxQuant]
−
|
+
|1.6.7.0-IGB-gcc-4.9.4
−
|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.
+
|MaxQuant is a proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data.  
 
|-
 
|-
−
|[https://www.ffmpeg.org/ FFmpeg]
+
|[https://github.com/mcveanlab/mccortex McCortex]
−
|3.3-IGB-gcc-4.9.4
+
|1.0.1-IGB-gcc-4.9.4
−
|A complete, cross-platform solution to record, convert and stream audio and video. - Homepage: https://www.ffmpeg.org/
+
|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.
 
|-
 
|-
−
|[https://dendropy.org/ DendroPy]
+
|[https://sourceforge.net/projects/meraculous20/ Meraculous-2d]
−
|4.4.0-IGB-gcc-4.9.4-Python-3.6.1
+
|2.2.6-IGB-gcc-4.9.4
−
|DendroPy is a Python library for phylogenetic computing.  
+
|Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements.
 
|-
 
|-
−
|[http://asperasoft.com/ aspera]
+
|[https://mesonbuild.com Meson]
−
|3.7.6
+
|0.51.2-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
 
|-
 
|-
−
|[https://github.com/PacificBiosciences/minorseq/blob/54ac795d7c119d21a4611d91ac458cd3e2e2b30a/doc/INSTALL.md minorseq]
+
|[https://bitbucket.org/berkeleylab/metabat MetaBAT]
−
|20180314-IGB-gcc-4.9.4
+
|2.12.1
−
|Minor Variant Calling and Phasing Tools
+
|MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
 
|-
 
|-
−
|zlib
+
|[http://metagene.nig.ac.jp/ MetaGeneAnnotator]
−
|
+
|20080819-x86-64
−
|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.
+
|MetaGeneAnnotator is a gene-finding program for prokaryote and phage.
 
|-
 
|-
−
|[https://www.agisoft.com/ metashape]
+
|[https://metavelvet.dna.bio.keio.ac.jp/ MetaVelvet]
−
|1.5.1-IGB-gcc-4.9.4
+
|1.2.02-IGB-gcc-4.9.4
−
|photogrammetricprocessing of digital images and 3D spatial data generation
+
|An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
 
|-
 
|-
−
|[https://genie.weizmann.ac.il/pubs/mir07/mir07_exe.html PITA]
+
|[https://www.continuum.io/anaconda-overview Miniconda2]
−
|6-IGB-gcc-4.9.4
+
|4.7.12.1
−
|The PITA executable allows you to identify and score microRNA targets on UTRs.
+
|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://github.com/genome/bam-readcount bam-readcount]
+
|Miniconda3
−
|0.8.0-IGB-gcc-4.9.4
+
|
−
|The purpose of this program is to generate metrics at single nucleotide positions.
+
|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://samtools.sourceforge.net tabix]
+
|Mono
−
|0.2.6-IGB-gcc-4.9.4
+
|
−
|Generic indexer for TAB-delimited genome position files
+
|An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
 
|-
 
|-
−
|[https://github.com/abyzovlab/CNVnator CNVnator]
+
|[http://www.mothur.org/ Mothur]
−
|0.3.3-IGB-gcc-4.9.4
+
|1.38.1.1<br>1.39.5<br>1.39.5-IGB-gcc-4.9.4
−
|a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
+
|Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
 
|-
 
|-
−
|[http://www.gurobi.com/ Gurobi]
+
|[http://multiqc.info/ MultiQC]
−
|7.5.2
+
|0.9-IGB-gcc-4.9.4-Python-2.7.13<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
−
|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.
+
|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.
 
|-
 
|-
−
|libreadline
+
|[http://www.nasm.us/ NASM]
−
|
+
|2.12.02-IGB-gcc-4.9.4
−
|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.
+
|NASM: General-purpose x86 assembler
 
|-
 
|-
−
|[http://www.gnu.org/software/coreutils/coreutils.html coreutils]
+
|[http://nco.sourceforge.net NCO]
−
|8.28-IGB-gcc-4.9.4
+
|4.7.2-IGB-gcc-4.9.4
−
|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.
+
|manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5
 
|-
 
|-
−
|JUnit
+
|[https://github.com/ncbi/ngs NGS]
−
|
+
|1.3.0-IGB-gcc-4.9.4
−
|A programmer-oriented testing framework for Java.
+
|NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. - Homepage: https://github.com/ncbi/ngs
 
|-
 
|-
−
|[http://younglab.wi.mit.edu/super_enhancer_code.html ROSE]
+
|[http://www.nwchem-sw.org NWChem]
−
|20150210-IGB-gcc-4.9.4-Python-2.7.13
+
|6.6.revision27746-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)
+
|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.
 
|-
 
|-
−
|[https://github.com/dellytools/delly delly]
+
|[https://github.com/wdecoster/NanoPlot NanoPlot]
−
|0.8.1-IGB-gcc-4.9.4
+
|1.18.2-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|Plotting tool for long read sequencing data and alignments.
 
|-
 
|-
−
|[http://qiime.org/ QIIME]
+
|[https://ccl.northwestern.edu/netlogo/ NetLogo]
−
|1.9.1
+
|5.2.1<br>6.0.3
−
|QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
+
|NetLogo is a multi-agent programmable modeling environment. It is used by many tens of thousands of students, teachers and researchers worldwide.
 
|-
 
|-
−
|[https://bitbucket.org/nsegata/graphlan/ graphlan]
+
|[https://ninja-build.org/ Ninja]
−
|6ca8735-IGB-gcc-4.9.4-Python-2.7.13
+
|1.9.0-IGB-gcc-4.9.4
−
|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.
+
|Ninja is a small build system with a focus on speed.
 
|-
 
|-
−
|[https://experts.illinois.edu/en/publications/truesight-self-training-algorithm-for-splice-junction-detection-u truesight]
+
|[http://nucleoatac.readthedocs.io/en/latest/ NucleoATAC]
−
|0.06-IGB-gcc-4.9.4
+
|0.3.4-IGB-gcc-4.9.4-Python-2.7.13
−
|A Self-training Algorithm for Splice Junction Detection using RNA-seq.
+
|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.
 
|-
 
|-
−
|[https://cran.r-project.org/web/packages/rgeos/index.html rgeos]
+
|[http://ocaml.org/ OCaml]
−
|0.4-2-IGB-gcc-4.9.4-R-3.5.0
+
|4.05.0-IGB-gcc-4.9.4
−
|nterface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries.
+
|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.
 
|-
 
|-
−
|[https://github.com/broadinstitute/cromwell cromwell]
+
|[https://github.com/brianbeliveau/OligoMiner OligoMiner]
−
|39-Java-1.8.0_152
+
|20181123-IGB-gcc-4.9.4
−
|Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
+
|A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
 
|-
 
|-
−
|GCCcore
+
|[http://xianyi.github.com/OpenBLAS/ OpenBLAS]
−
|
+
|0.2.19-GCC-4.9.4-2.28-LAPACK-3.7.0-test
−
|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,...).
+
|OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
 
|-
 
|-
−
|efiest/devlocal
+
|[http://openbabel.org OpenBabel]
−
|devlocal
+
|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.
 
|-
 
|-
−
|[http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Trim_Galore]
+
|[http://opencv.org/ OpenCV]
−
|0.4.4-IGB-gcc-4.9.4
+
|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
−
|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.
+
|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.maizegenetics.net/tassel TASSEL]
+
|[http://www.open-mpi.org/ OpenMPI]
−
|5.2.28-Java-1.8.0_121
+
|2.1.0-GCC-4.9.4-2.28<br>4.0.0-GCC-8.2.0-2.32
−
|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
+
|The Open MPI Project is an open source MPI-3 implementation.
 
|-
 
|-
−
|[http://www.coxdocs.org/doku.php?id=maxquant:start MaxQuant]
+
|OpenPGM
−
|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.
 
−
|-
 
−
|libgd
 
 
|
 
|
−
|GD is an open source code library for the dynamic creation of images by programmers. - Homepage: http://libgd.bitbucket.org/
+
|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://exon.gatech.edu/GeneMark/ GeneMark-ES]
+
|[https://github.com/davidemms/OrthoFinder OrthoFinder]
−
|4.33-IGB-gcc-4.9.4-Perl-5.24.1<br>4.33-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
+
|2.2.7<br>2.3.7-IGB-gcc-4.9.4
−
|Novel genomes can be analyzed by the program GeneMark-ES utilizing unsupervised training.
+
|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.  
 
|-
 
|-
−
|[https://github.com/taoliu/MACS/ MACS2]
+
|[http://orthomcl.org/ OrthoMCL]
−
|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
+
|2.0.9-IGB-gcc-4.9.4-Perl-5.24.1
−
|Model Based Analysis for ChIP-Seq data
+
|OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. - Homepage: http://orthomcl.org/
 
|-
 
|-
−
|Gdk-Pixbuf
+
|[http://wasabiapp.org/software/pagan PAGAN]
−
|
+
|20150723-IGB-gcc-4.9.4
−
|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.
+
|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.
 
|-
 
|-
−
|[http://lame.sourceforge.net/ LAME]
+
|[http://abacus.gene.ucl.ac.uk/software/paml.html PAML]
−
|3.99.5-IGB-gcc-4.9.4
+
|4.9e-IGB-gcc-4.9.4
−
|LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
+
|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
 
|-
 
|-
−
|[http://www.broadinstitute.org/software/discovar/blog/ DISCOVARdenovo]
+
|[https://github.com/neufeld/pandaseq PANDAseq]
−
|52488-IGB-gcc-4.9.4
+
|2.11-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.
+
|PANDAseq assembles Illumina Solexa overlapping pair-end reads. - Homepage: https://github.com/neufeld/pandaseq
 
|-
 
|-
−
|[https://www.continuum.io/anaconda-overview Miniconda2]
+
|PCRE
−
|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.
 
−
|-
 
−
|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.
+
|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/matthiasplappert/keras-rl keras-rl]
+
|[https://github.com/tbischler/PEAKachu PEAKachu]
−
|0.3.0-IGB-gcc-4.9.4-Python-2.7.13
+
|0.1.0-IGB-gcc-8.2.0-Python-3.7.2
−
|keras-rl implements some state-of-the art deep reinforcement learning algorithms in Python and seamlessly integrates with the deep learning library Keras.
+
|Peak calling tool for CLIP-seq data
 
|-
 
|-
−
|libdap
+
|[http://sco.h-its.org/exelixis/web/software/pear/ PEAR]
−
|
+
|0.9.8-IGB-gcc-4.9.4
−
|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.
+
|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/ncbi/ncbi-vdb ncbi-vdb]
+
|[https://github.com/soedinglab/PEnG-motif PEnG-motif]
−
|2.8.2-IGB-gcc-4.9.4
+
|1.0.1
−
|The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. - Homepage: https://github.com/ncbi/ncbi-vdb
+
|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/Kingsford-Group/scallop scallop]
+
|[http://picrust.github.io/picrust/ PICRUSt]
−
|0.10.3-IGB-gcc-4.9.4<br>0.10.4-IGB-gcc-4.9.4
+
|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
−
|Scallop is an accurate reference-based transcript assembler. Scallop features its high accuracy in assembling multi-exon transcripts as well as lowly expressed transcripts.
+
|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.
 
|-
 
|-
−
|Mono
+
|[https://genie.weizmann.ac.il/pubs/mir07/mir07_exe.html PITA]
−
|
+
|6-IGB-gcc-4.9.4
−
|An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
+
|The PITA executable allows you to identify and score microRNA targets on UTRs.
 
|-
 
|-
−
|[http://lbzip2.org/ lbzip2]
+
|[http://wasabiapp.org/software/prank/ PRANK]
−
|2.5-IGB-gcc-4.9.4
+
|170427-IGB-gcc-4.9.4
−
|lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format.
+
|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.
 
|-
 
|-
−
|help2man
+
|PROJ
 
|
 
|
−
|help2man produces simple manual pages from the --help and --version output of other commands.
+
|Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
 
|-
 
|-
−
|[http://nucleoatac.readthedocs.io/en/latest/ NucleoATAC]
+
|Pango
−
|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.
+
|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. - Homepage: http://www.pango.org/
 
|-
 
|-
−
|[http://www.lysator.liu.se/~nisse/nettle/ nettle]
+
|[https://github.com/shawnzhangyx/PePr PePr]
−
|3.3-IGB-gcc-4.9.4
+
|1.1.21-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|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
 +
|-
 +
|[http://www.perl.org/ Perl]
 +
|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
 +
|Larry Wall Practical Extraction and Report Language
 
|-
 
|-
−
|[https://github.com/baoe/AlignGraph AlignGraph]
+
|[https://github.com/kundajelab/phantompeakqualtools Phantompeaktools]
−
|20180222-IGB-gcc-4.9.4
+
|1.2-IGB-gcc-4.9.4-R-3.4.1
−
|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.
+
|Custom SPP for Phantompeaktools
 
|-
 
|-
−
|Yasm
+
|Phantompeaktools-spp
 
|
 
|
−
|Yasm: Complete rewrite of the NASM assembler with BSD license
+
|Custom SPP for Phantompeaktools
 
|-
 
|-
−
|[http://platanus.bio.titech.ac.jp/platanus-assembler platanus]
+
|[https://sourceforge.net/projects/phispy PhiSpy]
−
|1.2.4
+
|2.3-IGB-gcc-4.9.4-Python-2.7.13
−
|Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences ofhighly heterozygous diploids from massively parallel shotgun sequencing data.
+
|A novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies
−
|-
 
−
|[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.
 
 
|-
 
|-
−
|[http://owenjm.github.io/damidseq_pipeline/ damidseq]
+
|[https://github.com/gjospin/PhyloSift PhyloSift]
−
|1.4-IGB-gcc-4.9.4
+
|1.0.0_01-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.
+
|PhyloSift is a suite of software tools to conduct phylogeneticanalysis of genomes and metagenomes.
 
|-
 
|-
−
|[https://support.10xgenomics.com/genome-exome/software/visualization/latest/what-is-loupe loupe]
+
|[http://pillow.readthedocs.org/ Pillow]
−
|2.1.1
+
|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
−
|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.
+
|Pillow is the friendly PIL fork by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
 
|-
 
|-
−
|[http://metagene.nig.ac.jp/ MetaGeneAnnotator]
+
|[https://github.com/andyrimmer/Platypus Platypus]
−
|20080819-x86-64
+
|20180622-IGB-gcc-4.9.4-Python-2.7.13
−
|MetaGeneAnnotator is a gene-finding program for prokaryote and phage.
+
|The Platypus variant caller.  
 
|-
 
|-
−
|[https://sourceforge.net/projects/rdp-classifier RDPClassifier]
+
|[https://github.com/rrwick/Porechop Porechop]
−
|2.12-Java-1.8.0_152<br>2.2-Java-1.8.0_152
+
|0.2.3-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|Porechop is a tool for finding and removing adapters from Oxford Nanopore reads.
 
|-
 
|-
−
|[https://github.com/soedinglab/PEnG-motif PEnG-motif]
+
|[https://github.com/hyattpd/prodigal Prodigal]
−
|1.0.1
+
|2.6.3
−
|PEnG-motif is an open-source software package for searching statistically overrepresented motifs (position specific weight matrices, PWMs) in a set of DNA sequences.
+
|Fast, reliable protein-coding gene prediction for prokaryotic genomes.
 
|-
 
|-
−
|[https://ccb.jhu.edu/software/kraken/ Kraken]
+
|[https://github.com/uoregon-postlethwait/prost Prost]
−
|1.0-IGB-gcc-4.9.4
+
|0.7.45-IGB-gcc-4.9.4-Python-2.7.13
−
|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.  
+
|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).
 
|-
 
|-
−
|libxml2
+
|[https://mathema.tician.de/software/pycuda/ PyCUDA]
−
|
+
|2017.1-IGB-gcc-4.9.4-Python-2.7.13
−
|Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
+
|PyCUDA lets you access Nvidia‘s CUDA parallel computation API from Python. - Homepage: https://mathema.tician.de/software/pycuda/
 
|-
 
|-
−
|[https://github.com/PacificBiosciences/pb-assembly pb-assembly]
+
|[http://pytorch.org PyTorch]
−
|0.0.6
+
|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
−
|PacBio Assembly Tool Suite
+
|Tensors and Dynamic neural networks in Pythonwith strong GPU acceleration.
 
|-
 
|-
−
|[http://qualimap.bioinfo.cipf.es/ qualimap]
+
|[http://www.zeromq.org/bindings:python PyZMQ]
−
|2.2.1-Java-1.8.0_121
+
|16.0.2-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|Python bindings for ZeroMQ
 
|-
 
|-
−
|FFTW
+
|[https://github.com/pysam-developers/pysam Pysam]
−
|
+
|0.13.0-IGB-gcc-4.9.4-Python-2.7.13<br>0.13.0-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|Pysam is a python module for reading and manipulating Samfiles.  Its a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
 
|-
 
|-
−
|[http://tukaani.org/xz/ XZ]
+
|[http://python.org/ Python]
−
|5.2.3-IGB-gcc-4.9.4<br>5.2.3-IGB-gcc-8.2.0
+
|2.7.13-IGB-gcc-4.9.4<br>3.6.1-IGB-gcc-4.9.4<br>3.7.2-IGB-gcc-8.2.0
−
|xz: XZ utilities
+
|Python is a programming language that lets you work more quickly and integrate your systems more effectively.
 
|-
 
|-
−
|[https://www.kernel.org/pub/linux/utils/util-linux util-linux]
+
|[http://qiime.org/ QIIME]
−
|2.34-IGB-gcc-4.9.4
+
|1.9.1
−
|Set of Linux utilities
+
|QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
 
|-
 
|-
−
|[http://bowtie-bio.sourceforge.net/bowtie2/index.shtml Bowtie2]
+
|[http://qiime.org/ QIIME2]
−
|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
+
|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
−
|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.
+
|QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.
 
|-
 
|-
−
|[http://creskolab.uoregon.edu/stacks/ Stacks]
+
|[http://qt.io/ Qt]
−
|1.47-IGB-gcc-4.9.4
+
|4.8.7-IGB-gcc-4.9.4
−
|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.
+
|Qt is a comprehensive cross-platform C++ application framework.
 
|-
 
|-
−
|[http://www.gdal.org/ GDAL]
+
|[http://www.r-project.org/ R]
−
|2.3.1-IGB-gcc-4.9.4<br>3.0.3-IGB-gcc-8.2.0
+
|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
−
|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.
+
|R is a free software environment for statistical computing and graphics.
 
|-
 
|-
−
|[http://rpy.sourceforge.net/ rpy2]
+
|[https://github.com/stamatak/standard-RAxML RAxML]
−
|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>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
+
|8.2.12-IGB-gcc-4.9.4
−
|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.  
+
|RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
 
|-
 
|-
−
|[https://github.com/biocore/redbiom redbiom]
+
|[https://sourceforge.net/projects/rdp-classifier RDPClassifier]
−
|0.3.2-IGB-gcc-4.9.4-Python-3.6.1
+
|2.12-Java-1.8.0_152<br>2.2-Java-1.8.0_152
−
|Redbiom is a cache service for sample metadata and sample data.  
+
|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.
 
|-
 
|-
−
|[http://www.drive5.com/usearch/index.html USEARCH]
+
|[http://www.sanger.ac.uk/science/tools/reapr REAPR]
−
|11.0.667<br>6.1.544<br>7.0.1090<br>9.2.64
+
|1.0.18-IGB-gcc-4.9.4
−
|USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
+
|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://exon.gatech.edu/GeneMark/ GeneMarkS]
+
|[http://eddylab.org/software/recon/ RECON]
−
|4.30-IGB-gcc-4.9.4
+
|1.08-IGB-gcc-4.9.4-Perl-5.24.1
−
|GeneMarkS: a self-training method for prediction of gene starts in microbial genomes
+
|a package for automated de novo identification of repeat families from genomic sequences
 
|-
 
|-
−
|[https://github.com/dstreett/FLASH2 FLASH2]
+
|[https://github.com/slowkoni/rfmix RFMix]
−
|2.2.00-IGB-gcc-4.9.4
+
|20180503-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.
+
|A discriminative method for local ancestry inference
 
|-
 
|-
−
|argtable
+
|[http://www.regulatory-genomics.org/rgt/basic-introduction/ RGT]
−
|
+
|0.11.3-IGB-gcc-4.9.4-Python-2.7.13
−
|Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. - Homepage: http://argtable.sourceforge.net/
+
|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.  
 
|-
 
|-
−
|[https://github.com/cboursnell/crb-blast crb-blast]
+
|[http://www.repeatmasker.org/RMBlast.html RMBlast]
−
|0.6.9-IGB-gcc-4.9.4
+
|2.6.0-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.
+
|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.
 
|-
 
|-
−
|[http://ccb.jhu.edu/software/stringtie/gff.shtml gffread]
+
|[https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid RNAhybrid]
−
|ba7535f-IGB-gcc-4.9.4
+
|2.1.2-IGB-gcc-4.9.4
−
|The program gffread can be used to validate, filter, convert and perform various other operations on GFF files
+
|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://qt.io/ Qt]
+
|[http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer RNAmmer]
−
|4.8.7-IGB-gcc-4.9.4
+
|1.2-IGB-gcc-4.9.4-Perl-5.24.1
−
|Qt is a comprehensive cross-platform C++ application framework.
+
|Ribosomal RNA sub units
 
|-
 
|-
−
|[https://www.ebi.ac.uk/interpro/interproscan.html InterProScan]
+
|[http://rna.urmc.rochester.edu/RNAstructure.html RNAstructure]
−
|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
+
|6.0-IGB-gcc-4.9.4
−
|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.
+
|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://github.com/Ensembl/ensembl-vep VEP]
+
|[http://younglab.wi.mit.edu/super_enhancer_code.html ROSE]
−
|92.4-IGB-gcc-4.9.4-Perl-5.24.1
+
|20150210-IGB-gcc-4.9.4-Python-2.7.13
−
|VEP (Variant Effect Predictor) predicts the functional effects of genomic variants.
+
|To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam)
 
|-
 
|-
−
|HarfBuzz
+
|[http://download.rsat.eu/ RSAT]
−
|
+
|2018-08-04-IGB-gcc-4.9.4
−
|HarfBuzz is an OpenType text shaping engine. - Homepage: http://www.freedesktop.org/wiki/Software/HarfBuzz
+
|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
 
|-
 
|-
−
|[https://bitbucket.org/antismash/antismash/ antismash]
+
|[http://deweylab.github.io/RSEM/ RSEM]
−
|4.1.0
+
|1.3.0-IGB-gcc-4.9.4<br>1.3.1-IGB-gcc-4.9.4
−
|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.
+
|RNA-Seq by Expectation-Maximization
 
|-
 
|-
−
|[https://github.com/data61/gossamer gossamer]
+
|[http://rseqc.sourceforge.net/ RSeQC]
−
|20170105-IGB-gcc-4.9.4
+
|2.6.4-IGB-gcc-4.9.4-Python-2.7.13
−
|The gossamer bioinformatics suite contains goss, gossple, xenome, and electus
+
|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.
 
|-
 
|-
−
|libevent
+
|[http://fenderglass.github.io/Ragout/ Ragout]
−
|
+
|2.0-IGB-gcc-4.9.4
−
|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.
+
|Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references.  
 
|-
 
|-
−
|flex
+
|[https://cran.r-project.org/web/packages/RcppGSL/index.html RcppGSL]
−
|
+
|0.3.2-IGB-gcc-4.9.4-R-3.3.3
−
|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.
+
|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.
 
|-
 
|-
−
|pixman
+
|[http://www.repeatmasker.org/ RepeatMasker]
−
|
+
|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
−
|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.
+
|RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.  
 
|-
 
|-
−
|[http://tensorly.org/stable/home.html tensorly]
+
|[http://www.repeatmasker.org/RepeatModeler/ RepeatModeler]
−
|0.4.2-IGB-gcc-4.9.4-Python-3.6.1
+
|1.0.11-IGB-gcc-4.9.4-Perl-5.24.1
−
|Simple and Fast Tensor Learning in Python
+
|1.0.11
 
|-
 
|-
−
|[http://hibberdlab.com/transrate/ transrate]
+
|[http://www.repeatmasker.org/RepeatModeler/ RepeatScout]
−
|1.0.3
+
|1.0.5-IGB-gcc-4.9.4
−
|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.
+
|De Novo Repeat Finder,
 +
|-
 +
|[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://www.ruby-lang.org 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.
 
|-
 
|-
−
|[https://github.com/tbischler/PEAKachu PEAKachu]
+
|[https://www.rust-lang.org Rust]
−
|0.1.0-IGB-gcc-8.2.0-Python-3.7.2
+
|1.41.1<br>1.41.1-IGB-gcc-8.2.0
−
|Peak calling tool for CLIP-seq data
+
|Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
 
|-
 
|-
−
|[http://software.broadinstitute.org/software/igv/ igv]
+
|[http://www.htslib.org/ SAMtools]
−
|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
+
|0.1.20-IGB-gcc-4.9.4<br>1.10-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
−
|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.
+
|SAM Tools provide various utilities for manipulating alignments in the SAM format,  including sorting, merging, indexing and generating alignments in a per-position format.
 
|-
 
|-
−
|[https://bibiserv2.cebitec.uni-bielefeld.de/rnahybrid RNAhybrid]
+
|[http://www.scons.org/ SCons]
−
|2.1.2-IGB-gcc-4.9.4
+
|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
−
|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.  
+
|SCons is a software construction tool.
 
|-
 
|-
 
|[http://www.libsdl.org/ SDL2]
 
|[http://www.libsdl.org/ SDL2]
Line 1,037: Line 1,073:
 
|SDL: Simple DirectMedia Layer, a cross-platform multimedia library
 
|SDL: Simple DirectMedia Layer, a cross-platform multimedia library
 
|-
 
|-
−
|libjpeg-turbo
+
|[https://github.com/smirarab/sepp SEPP]
−
|
+
|20180223-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
 
|-
 
|-
−
|[http://www.imagemagick.org/ ImageMagick]
+
|[https://github.com/ruanjue/smartdenovo SMARTdenovo]
−
|7.0.5-5-IGB-gcc-4.9.4
+
|20170916-IGB-gcc-4.9.4-Perl-5.24.1
−
|ImageMagick is a software suite to create, edit, compose, or convert bitmap images - Homepage: http://www.imagemagick.org/
+
|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.
 
|-
 
|-
−
|[http://www.htslib.org/ BCFtools]
+
|[http://korflab.ucdavis.edu/software.html SNAP]
−
|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
+
|2013-11-29-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
+
|(Semi-HMM-based Nucleic Acid Parser) gene prediction tool
 
|-
 
|-
−
|[https://github.com/sparsehash/sparsehash sparsehash]
+
|[http://snver.sourceforge.net/ SNVer]
−
|2.0.3-IGB-gcc-4.9.4
+
|0.5.3-Java-1.8.0_121<br>0.5.3-Java-1.8.0_152
−
|This directory contains several hash-map implementations, similar inAPI to SGIs hash_map class, but with different performance characteristics.
+
|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.  
 
|-
 
|-
−
|[https://github.com/maasha/biopieces Biopieces]
+
|[http://soap.genomics.org.cn/SOAPdenovo-Trans.html SOAPdenovo-Trans]
−
|2.0-IGB-gcc-4.9.4-Perl-5.24.1
+
|1.03
−
|Biopieces is a bioinformatic framework of tools easily used and easily created.
+
|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.  
 
|-
 
|-
−
|[https://www.nextflow.io/ nextflow]
+
|[http://cab.spbu.ru/software/spades/ SPAdes]
−
|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
+
|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
−
|Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.  
+
|SPAdes . St. Petersburg genome assembler . is intended for both standard isolates and single-cell MDA bacteria assemblies.
 
|-
 
|-
−
|[http://genome.cse.ucsc.edu kentUtils]
+
|[http://www.sqlite.org/ SQLite]
−
|353-IGB-gcc-4.9.4
+
|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
−
|UCSC genome browser kent bioinformatic utilities
+
|SQLite: SQL Database Engine in a C Library
 
|-
 
|-
−
|[https://github.com/hyattpd/prodigal Prodigal]
+
|[http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std SRA-Toolkit]
−
|2.6.3
+
|2.8.2-1
−
|Fast, reliable protein-coding gene prediction for prokaryotic genomes.
+
|The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format  - Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std
 
|-
 
|-
−
|CMake
+
|[https://github.com/alexdobin/STAR STAR]
−
|
+
|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>2.7.3a-IGB-gcc-8.2.0
−
|CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
+
|STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
 
|-
 
|-
−
|[https://github.com/lh3/seqtk/ seqtk]
+
|[https://github.com/STAR-Fusion/STAR-Fusion/wiki STAR-Fusion]
−
|1.2-IGB-gcc-4.9.4<br>1.2-IGB-gcc-8.2.0<br>1.3-IGB-gcc-8.2.0
+
|1.6.0-IGB-gcc-4.9.4
−
|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.
+
|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://developer.nvidia.com/cuda-toolkit CUDA]
+
|[http://computation.llnl.gov/projects/sundials SUNDIALS]
−
|10.0.130<br>8.0.61<br>8.0.61-IGB-gcc-4.9.4<br>9.0.176-IGB-gcc-4.9.4<br>9.1.85
+
|2.6.2-IGB-gcc-4.9.4
−
|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.
+
|SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
 
|-
 
|-
−
|file
+
|[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
−
|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.
+
|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/
 
|-
 
|-
−
|[http://www.bzip.org/ bzip2]
+
|[https://github.com/COMBINE-lab/salmon Salmon]
−
|1.0.6-IGB-gcc-4.9.4<br>1.0.6-IGB-gcc-8.2.0
+
|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
−
|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.
+
|Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
 
|-
 
|-
−
|[https://github.com/PacificBiosciences/unanimity/ unanimity]
+
|[https://github.com/COMBINE-lab/SalmonTools SalmonTools]
−
|20180307-IGB-gcc-4.9.4
+
|20190604-IGB-gcc-8.2.0
−
|C++ library and its applications to generate and process accurate consensus sequences
+
|Useful tools for working with Salmon output
 
|-
 
|-
−
|[http://vfsmspineagent.fsm.northwestern.edu/ Spine]
+
|ScaLAPACK
−
|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.
+
|The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
 
|-
 
|-
−
|[https://github.com/gpertea/stringtie stringtie]
+
|[https://www.pmgenomics.ca/hoffmanlab/proj/segway/ Segway]
−
|2.1.1-IGB-gcc-4.9.4
+
|2.0.1-IGB-gcc-4.9.4-Python-2.7.13
−
|Transcript assembly and quantification for RNA-Seq
+
|Segway is a tool for easy pattern discovery and identification in functional genomics data.
 
|-
 
|-
−
|[https://github.com/nanoporetech/pomoxis pomoxis]
+
|[https://github.com/bioinf/Sibelia Sibelia]
−
|0.1.0-IGB-gcc-4.9.4-Python-3.6.1
+
|3.0.7-IGB-gcc-4.9.4
−
|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.
+
|Sibelia is a tool for finding synteny blocks in closely related genomes, like different strains of the same bacterial species.
 
|-
 
|-
−
|[http://soap.genomics.org.cn/SOAPdenovo-Trans.html SOAPdenovo-Trans]
+
|[http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp SignalP]
−
|1.03
+
|4.1
−
|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.
+
|Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
 
|-
 
|-
−
|[http://glaros.dtc.umn.edu/gkhome/metis/metis/overview METIS]
+
|[http://http://sox.sourceforge.net/ SoX]
−
|5.1.0-IGB-gcc-4.9.4
+
|14.4.2-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.
+
|Sound eXchange, the Swiss Army knife of audio manipulation
 
|-
 
|-
−
|[https://www.ks.uiuc.edu/Research/vmd/ VMD]
+
|[http://vfsmspineagent.fsm.northwestern.edu/ Spine]
−
|1.9.3-IGB-gcc-4.9.4
+
|0.2.1-IGB-gcc-4.9.4
−
|VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.  
+
|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.
 
|-
 
|-
−
|hwloc
+
|[http://creskolab.uoregon.edu/stacks/ Stacks]
−
|
+
|1.47-IGB-gcc-4.9.4
−
|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.
+
|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.
 
|-
 
|-
−
|[https://github.com/soedinglab/bamm-suite bamm-suite]
+
|[http://ccb.jhu.edu/software/stringtie/ StringTie]
−
|20191127-IGB-gcc-4.9.4-Python-3.6.1
+
|1.3.3-IGB-gcc-4.9.4<br>1.3.6-IGB-gcc-4.9.4
−
|BaMM-suite is the motif finding suite developed by the Soedinglab.
+
|StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
 
|-
 
|-
−
|[https://github.com/HAugustijn/BiG-MAP2 big-map2-analyse]
+
|[http://subread.sourceforge.net/ Subread]
−
|20200124
+
|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
−
|This is the Github repository for the Biosynthetic Gene cluster Meta’omics abundance Profiler
+
|High performance read alignment, quantification and mutation discovery
 
|-
 
|-
−
|[http://www.gtk.org/ GLib]
+
|[http://faculty.cse.tamu.edu/davis/suitesparse.html SuiteSparse]
−
|2.62.3-IGB-gcc-4.9.4
+
|5.4.0-IGB-gcc-4.9.4-METIS-5.1.0
−
|GLib is one of the base libraries of the GTK+ project
+
|SuiteSparse is a collection of libraries manipulate sparse matrices.
 
|-
 
|-
−
|[https://github.com/arq5x/bedtools2 BEDTools]
+
|[https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Supernova]
−
|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
+
|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
−
|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.
+
|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://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std SRA-Toolkit]
+
|Szip
−
|2.8.2-1
+
|
−
|The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format  - Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std
+
|Szip compression software, providing lossless compression of scientific data
 
|-
 
|-
−
|[https://www.tbi.univie.ac.at/RNA/ ViennaRNA]
+
|[http://www.maizegenetics.net/tassel TASSEL]
−
|2.4.2-IGB-gcc-4.9.4
+
|5.2.28-Java-1.8.0_121
−
|The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
+
|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://mariadb.org/ MariaDB]
+
|[http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm TMHMM]
−
|10.1.31-IGB-gcc-4.9.4<br>10.1.31-IGB-gcc-8.2.0<br>5.5.58-IGB-gcc-4.9.4
+
|2.0c-IGB-gcc-4.9.4
−
|MariaDB An enhanced, drop-in replacement for MySQL.
+
|Transmembrane helices in proteins
 +
|-
 +
|[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.
 
|-
 
|-
−
|xorg-macros
+
|Tcl
 
|
 
|
−
|X.org macros utilities.
+
|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/mateidavid/fast5 fast5]
+
|[https://github.com/tensorflow/models TensorFlowModels]
−
|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
+
|1.11-IGB-gcc-4.9.4-Python-3.6.1<br>20171113-IGB-gcc-4.9.4-Python-3.6.1
−
|A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
+
|This repository contains a number of different models implemented in TensorFlow:
 
|-
 
|-
−
|[http://wasabiapp.org/software/pagan PAGAN]
+
|[https://www.tensorflow.org/ Tensorflow]
−
|20150723-IGB-gcc-4.9.4
+
|1.2.1-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|An open-source software library for Machine Intelligence
 
|-
 
|-
−
|[http://nco.sourceforge.net NCO]
+
|[https://www.tensorflow.org/ Tensorflow-GPU]
−
|4.7.2-IGB-gcc-4.9.4
+
|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
−
|manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5
+
|An open-source software library for Machine Intelligence
 
|-
 
|-
−
|[https://github.com/barricklab/breseq breseq]
+
|[http://deeplearning.net/software/theano Theano]
−
|0.31.0-IGB-gcc-4.9.4
+
|0.9.0-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|Theano is a Python library that allows you to define, optimize,and evaluate mathematical expressions involving multi-dimensional arrays efficiently. - Homepage: http://deeplearning.net/software/theano
 
|-
 
|-
−
|efiest/efitools
+
|Tk
−
|efitools/devlocal
 
 
|
 
|
 +
|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://bioinform.github.io/breakseq2/ BreakSeq2]
+
|[http://ccb.jhu.edu/software/tophat/index.shtml TopHat]
−
|2.2-IGB-gcc-4.9.4-Python-2.7.13
+
|1.4.1<br>2.1.1-IGB-gcc-4.9.4
−
|Ultrafast and accurate nucleotide-resolution analysis of structural variants - Homepage: http://bioinform.github.io/breakseq2/
+
|TopHat is a fast splice junction mapper for RNA-Seq reads.
 
|-
 
|-
−
|[https://sourceforge.net/projects/meraculous20/ Meraculous-2d]
+
|[https://github.com/torch/distro Torch]
−
|2.2.6-IGB-gcc-4.9.4
+
|20171018-IGB-gcc-4.9.4-Python-3.6.1
−
|Meraculous-2D is a whole genome assembler for NGS reads (Illumina) that is capable of assembling large, diploid genomes with modest computational requirements.
+
|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/mirnylab/pairtools pairtools]
+
|[https://github.com/TransDecoder/TransDecoder/wiki TransDecoder]
−
|0.3.0-IGB-gcc-4.9.4-Python-3.6.1
+
|5.1.0-IGB-gcc-4.9.4-Perl-5.24.1
−
|pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment.
+
|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.
 
|-
 
|-
−
|[https://github.com/arq5x/poretools poretools]
+
|[http://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ Trim_Galore]
−
|0.6.0-IGB-gcc-4.9.4-Python-2.7.13
+
|0.4.4-IGB-gcc-4.9.4
−
|a toolkit for working with nanopore sequencing data from Oxford Nanopore. - Homepage: https://github.com/arq5x/poretools
+
|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://lomereiter.github.io/sambamba/ sambamba]
+
|[http://www.usadellab.org/cms/?page=trimmomatic Trimmomatic]
−
|0.6.6
+
|0.36-Java-1.8.0_121<br>0.36-Java-1.8.0_152<br>0.38-Java-1.8.0_152
−
|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.
+
|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://java.com/ Java]
+
|[http://trinityrnaseq.github.io/ Trinity]
−
|1.8.0_121<br>1.8.0_152<br>1.8.0_201<br>11.0.5
+
|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
−
|Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
+
|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://mesonbuild.com Meson]
+
|[https://trinotate.github.io/ Trinotate]
−
|0.51.2-IGB-gcc-4.9.4-Python-3.6.1
+
|3.1.1-IGB-gcc-4.9.4-Perl-5.24.1
−
|Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
+
|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.
 
|-
 
|-
−
|[https://github.com/BSSeeker/BSseeker2 BS-Seeker]
+
|[http://www.drive5.com/usearch/index.html USEARCH]
−
|2.1.2-IGB-gcc-4.9.4-Python-2.7.13
+
|11.0.667<br>6.1.544<br>7.0.1090<br>9.2.64
−
|BS Seeker 2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated short reads.
+
|USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
 
|-
 
|-
−
|[http://perfsuite.ncsa.illinois.edu/ perfsuite]
+
|[https://github.com/rrwick/Unicycler Unicycler]
−
|1.1.4-IGB-gcc-4.9.4
+
|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
−
|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).  
+
|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.
 
|-
 
|-
−
|[https://daler.github.io/pybedtools/main.html pybedtools]
+
|[http://www.cse.lehigh.edu/~chen/software.htm VASP-E]
−
|0.7.10-IGB-gcc-4.9.4-Python-3.6.1
+
|20190225-IGB-gcc-4.9.4<br>20191112-IGB-gcc-4.9.4
−
|pybedtools is a Python package that wraps BEDTools, so you will need both installed.
+
|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.
 
|-
 
|-
−
|[https://github.com/mitoNGS/MToolBox MToolBox]
+
|[https://vcftools.github.io VCFtools]
−
|1.0-IGB-gcc-4.9.4<br>1.2.1-IGB-gcc-4.9.4
+
|0.1.15-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.
+
|The aim of VCFtools is to provide  easily accessible methods for working with complex  genetic variation data in the form of VCF files. - Homepage: https://vcftools.github.io
 
|-
 
|-
−
|[https://bitbucket.org/liulab/mageck-vispr mageck-vispr]
+
|[https://github.com/Ensembl/ensembl-vep VEP]
−
|0.5.4-IGB-gcc-4.9.4-Python-3.6.1
+
|92.4-IGB-gcc-4.9.4-Perl-5.24.1
−
|MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
+
|VEP (Variant Effect Predictor) predicts the functional effects of genomic variants.
 
|-
 
|-
−
|[http://deeplearning.net/software/theano Theano]
+
|[https://github.com/IGBIllinois/VICSIN VICSIN]
−
|0.9.0-IGB-gcc-4.9.4-Python-2.7.13
+
|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>dev
−
|Theano is a Python library that allows you to define, optimize,and evaluate mathematical expressions involving multi-dimensional arrays efficiently. - Homepage: http://deeplearning.net/software/theano
+
|VICSIN = Viral, Integrative, and Conjugative Sequence Identification and Networking
 
|-
 
|-
−
|[https://github.com/jts/nanopolish nanopolish]
+
|[https://www.ks.uiuc.edu/Research/vmd/ VMD]
−
|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>0.6.0-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
+
|1.9.3-IGB-gcc-4.9.4
−
|Software package for signal-level analysis of Oxford Nanopore sequencing data.
+
|VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting.  
 
|-
 
|-
−
|[https://github.com/ginolhac/mapDamage mapDamage]
+
|[https://github.com/torognes/vsearch VSEARCH]
−
|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
+
|2.4.3-IGB-gcc-4.9.4
−
|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.
+
|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
 
|-
 
|-
−
|libpciaccess
+
|VarScan
 +
|2.3.9-Java-1.8.0_152
 
|
 
|
−
|Generic PCI access library.
 
 
|-
 
|-
−
|[https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html shapeit]
+
|[https://www.tbi.univie.ac.at/RNA/ ViennaRNA]
−
|2.20
+
|2.4.2-IGB-gcc-4.9.4
−
|SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
+
|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.
 +
|-
 +
|[http://tukaani.org/xz/ XZ]
 +
|5.2.3-IGB-gcc-4.9.4<br>5.2.3-IGB-gcc-8.2.0
 +
|xz: XZ utilities
 +
|-
 +
|Yasm
 +
|
 +
|Yasm: Complete rewrite of the NASM assembler with BSD license
 +
|-
 +
|[http://www.zeromq.org/ ZeroMQ]
 +
|4.2.2-IGB-gcc-4.9.4
 +
|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://www-inf.enst.fr/~demaille/a2ps/ a2ps]
 +
|4.14-IGB-gcc-4.9.4
 +
|a2ps-4.14: Formats an ascii file for printing on a postscript printer
 
|-
 
|-
 
|[http://www.genetics.ucla.edu/software/admixture/index.html admixture]
 
|[http://www.genetics.ucla.edu/software/admixture/index.html admixture]
Line 1,245: Line 1,305:
 
|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.  
 
|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://www.repeatmasker.org/RepeatModeler/ RepeatModeler]
+
|[https://nanoporetech.com/ albacore]
−
|1.0.11-IGB-gcc-4.9.4-Perl-5.24.1
+
|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
−
|1.0.11
+
|Local basecalling for MinKNOW
 
|-
 
|-
−
|[https://github.com/alticelabs/kyoto kyoto]
+
|[http://ant.apache.org/ ant]
−
|20170410-IGB-gcc-4.9.4
+
|1.10.1-Java-1.8.0_121<br>1.10.1-Java-1.8.0_152
−
|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:
+
|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.
 
|-
 
|-
−
|[http://bio-bwa.sourceforge.net/ BWA]
+
|[https://bitbucket.org/antismash/antismash/ antismash]
−
|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
+
|4.1.0
−
|Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
+
|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.
 
|-
 
|-
−
|[https://github.com/pezmaster31/bamtools BamTools]
+
|[http://merenlab.org/software/anvio/ anvio]
−
|2.4.1-IGB-gcc-4.9.4<br>2.5.1-IGB-gcc-4.9.4
+
|5.5-IGB-gcc-4.9.4-Python-3.6.1<br>6.1-IGB-gcc-4.9.4-Python-3.6.1
−
|BamTools provides both a programmers API and an end-users toolkit for handling BAM files.
+
|Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.
 
|-
 
|-
−
|[https://github.com/cschin/Peregrine Peregrine]
+
|argtable
−
|1.5.4
 
−
|Peregrine & SHIMMER Genome Assembly Toolkit
 
−
|-
 
−
|efiest/prod_private
 
−
|prod_private
 
 
|
 
|
 +
|Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss.  - Homepage: http://argtable.sourceforge.net/
 
|-
 
|-
−
|[https://github.com/soedinglab/hh-suite hhsuite]
+
|[http://asperasoft.com/ aspera]
−
|3.2.0
+
|3.7.6
−
|The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models
+
|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.
 
|-
 
|-
−
|[https://ccl.northwestern.edu/netlogo/ NetLogo]
+
|[http://atactk.readthedocs.io/ atactk]
−
|5.2.1<br>6.0.3
+
|0.1.6-IGB-gcc-4.9.4-Python-2.7.13
−
|NetLogo is a multi-agent programmable modeling environment. It is used by many tens of thousands of students, teachers and researchers worldwide.
+
|a toolkit for ATAC-seq data
 
|-
 
|-
−
|[http://www.bioperl.org/ BioPerl]
+
|[http://bioinf.uni-greifswald.de/augustus/ augustus]
−
|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
+
|3.2.3-IGB-gcc-4.9.4<br>3.3.2-IGB-gcc-4.9.4
−
|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.
+
|AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.  
 
|-
 
|-
−
|[https://github.com/DReichLab/EIG eigensoft]
+
|[https://aws.amazon.com/cli/ awscli]
−
|7.2.1-IGB-gcc-4.9.4
+
|1.16.113-IGB-gcc-4.9.4-Python-3.6.1
−
|The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006).  
+
|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.ncbi.nlm.nih.gov/genbank/tbl2asn2/ tbl2asn]
+
|[https://github.com/genome/bam-readcount bam-readcount]
−
|20180516<br>20190117<br>20200203
+
|0.8.0-IGB-gcc-4.9.4
−
|Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank
+
|The purpose of this program is to generate metrics at single nucleotide positions.
 
|-
 
|-
−
|[https://github.com/soedinglab/plass plass]
+
|[https://github.com/soedinglab/bamm-suite bamm-suite]
−
|2-c7e35-IGB-gcc-4.9.4<br>3-764a3
+
|20191127-IGB-gcc-4.9.4-Python-3.6.1
−
|Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.  
+
|BaMM-suite is the motif finding suite developed by the Soedinglab.
 
|-
 
|-
−
|[https://github.com/bioinf/Sibelia Sibelia]
+
|[http://dna.ku.dk/%7Esapfo/bammds.html bammds]
−
|3.0.7-IGB-gcc-4.9.4
+
|20140602-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.
+
|Software that allows to create a multidimensional scaling (MDS) plot of populations for genetic data.
 
|-
 
|-
−
|[https://github.com/rrwick/Unicycler Unicycler]
+
|[https://github.com/tseemann/barrnap barrnap]
−
|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
+
|0.9-IGB-gcc-4.9.4
−
|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.
+
|Barrnap predicts the location of ribosomal RNA genes in genomes.  
 
|-
 
|-
−
|[http://meme-suite.org/ MEME]
+
|[https://github.com/PacificBiosciences/bax2bam bax2bam]
−
|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
+
|20171114-IGB-gcc-4.9.4
−
|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.
+
|bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAMbasecall format.  
 
|-
 
|-
−
|[https://bitbucket.org/nygcresearch/treemix treemix]
+
|[http://bazel.io/ bazel]
−
|1.13-IGB-gcc-4.9.4
+
|0.6.0-Java-1.8.0_121
−
|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.
+
|Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Googles software.
 
|-
 
|-
−
|[https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome Supernova]
+
|[http://www.meilerlab.org/index.php/bclcommons/show/b_apps_id/1 bcl]
−
|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
+
|4.0.0
−
|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://www.biopython.org Biopython]
+
|[https://faculty.washington.edu/browning/beagle/beagle.html beagle]
−
|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-8.2.0-Python-3.7.2
+
|03Jul18.40b-Java-1.8.0_152
−
|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.  
+
|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.  
 
|-
 
|-
−
|[http://www.graphviz.org/ graphviz]
+
|[https://bedops.readthedocs.io/en/latest/ bedops]
−
|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.
 
−
|-
 
−
|[http://micans.org/mcl/ MCL]
 
−
|14.137-IGB-gcc-4.9.4
 
−
|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.  - Homepage: http://micans.org/mcl/
 
−
|-
 
−
|[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://bedops.readthedocs.io/en/latest/ bedops]
 
 
|2.4.30
 
|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.  
 
|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://trinotate.github.io/ Trinotate]
+
|[https://github.com/HAugustijn/BiG-MAP2 big-map2-analyse]
−
|3.1.1-IGB-gcc-4.9.4-Perl-5.24.1
+
|20200124
−
|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.
+
|This is the Github repository for the Biosynthetic Gene cluster Meta’omics abundance Profiler
 
|-
 
|-
−
|[https://github.com/uoregon-postlethwait/prost Prost]
+
|[https://github.com/HAugustijn/BiG-MAP2 big-map2-process]
−
|0.7.45-IGB-gcc-4.9.4-Python-2.7.13
+
|20200124
−
|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).
+
|This is the Github repository for the Biosynthetic Gene cluster Meta’omics abundance Profiler
 
|-
 
|-
−
|[http://sourceforge.net/projects/libuuid/ LibUUID]
+
|binutils
−
|1.0.3-IGB-gcc-4.9.4
+
|
−
|Portable uuid C library
+
|binutils: GNU binary utilities
 
|-
 
|-
−
|[https://sourceforge.net/projects/quast/ quast]
+
|[https://github.com/lmrodriguezr/rocker bio-rocker]
−
|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
+
|1.2.0-IGB-gcc-4.9.4-Ruby-2.4.2
−
|QUAST performs fast and convenient quality evaluation and comparison of genome assemblies.  
+
|Accurately detecting functional genes in metagenomes.
 
|-
 
|-
−
|[https://github.com/brentp/pyfasta/ pyfasta]
+
|[https://github.com/IGBIllinois/biodatabase/ biodatabase]
−
|0.5.2-IGB-gcc-4.9.4-Python-2.7.13
+
|1.0-IGB-gcc-4.9.4
−
|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.
+
|Scripts to create databases on the biodatabase machine.
 
|-
 
|-
−
|[https://github.com/broadinstitute/pilon pilon]
+
|[http://biom-format.org/ biom-format]
−
|1.22-Java-1.8.0_121<br>1.23-Java-1.8.0_152
+
|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
−
|Pilon is a software tool which can be used to:- Automatically improve draft assemblies- Find variation among strains, including large event detection
+
|The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables.
 
|-
 
|-
−
|udunits
+
|[https://github.com/DRL/blobtools blobtools]
−
|
+
|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
−
|UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
+
|Application for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots
 
|-
 
|-
−
|[https://github.com/cocodataset/cocoapi cocoapi]
+
|[https://github.com/barricklab/breseq breseq]
−
|20190218-IGB-gcc-4.9.4-Python-3.6.1
+
|0.31.0-IGB-gcc-4.9.4
−
|OCO is a large image dataset designed for object detection, segmentation, person keypoints detection, stuff segmentation, and caption generation.
+
|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.
 
|-
 
|-
−
|[https://www.synapse.org/ synapseclient]
+
|[http://invisible-island.net/byacc/byacc.html byacc]
−
|1.9.2-IGB-gcc-4.9.4-Python-3.6.1
+
|20170709-IGB-gcc-4.9.4
−
|Synapse is an open source software platform that data scientists can use to carry out, track, and communicate their research in real time.
+
|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.
 
|-
 
|-
−
|[https://github.com/MikkelSchubert/adapterremoval AdapterRemoval]
+
|[http://www.bzip.org/ bzip2]
−
|2.1.7-IGB-gcc-4.9.4
+
|1.0.6-IGB-gcc-4.9.4<br>1.0.6-IGB-gcc-8.2.0
−
|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.  
+
|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.
 
|-
 
|-
−
|[http://www.primer3.org primer3]
+
|cURL
−
|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.  
+
|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/vcflib/vcflib vcflib]
+
|[https://github.com/ComparativeGenomicsToolkit/cactus cactus]
−
|1.0.0-rc2-IGB-gcc-8.2.0
+
|20180705-IGB-gcc-4.9.4-Python-2.7.13
−
|a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
+
|Cactus is a reference-free whole-genome multiple alignment program.
 
|-
 
|-
−
|[https://github.com/soedinglab/BaMMmotif2 BaMMmotif]
+
|cairo
−
|2.0
 
−
|Bayesian Markov Model motif discovery software (version 2).
 
−
|-
 
−
|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.
+
|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://research-pub.gene.com/gmap/ GMAP-GSNAP]
+
|[https://github.com/gpertea/cdbfasta cdbfasta]
−
|2017-11-15-IGB-gcc-4.9.4
+
|20170316-IGB-gcc-4.9.4
−
|GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
+
|CDB (Constant DataBase) indexing and retrieval tools for FASTA files
 
|-
 
|-
−
|[https://bitbucket.org/nsegata/phylophlan/wiki/phylophlan2 phylophlan2]
+
|[https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger cellranger]
−
|0.34-IGB-gcc-4.9.4-Python-3.6.1
+
|2.1.0<br>2.1.1<br>3.0.0<br>3.0.1<br>3.1.0
−
|PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
+
|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://454.com/products/analysis-software/index.asp 454]
+
|[https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac cellranger-atac]
−
|2.8
+
|1.1.0
−
|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
+
|Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.  
 
|-
 
|-
−
|[http://compression.ca/pbzip2/ pbzip2]
+
|[https://ccb.jhu.edu/software/centrifuge/ centrifuge]
−
|1.1.13-IGB-gcc-4.9.4
+
|1.0.3-beta-IGB-gcc-4.9.4<br>1.0.4-beta-IGB-gcc-4.9.4
−
|PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines.
+
|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://cython.org/ Cython]
+
|[https://bitbucket.org/valenlab/chopchop chopchop]
−
|0.27.3-IGB-gcc-4.9.4-Python-2.7.13
+
|20190211-IGB-gcc-4.9.4-Python-2.7.13
−
|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.  
+
|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.
 
|-
 
|-
−
|[http://www.regulatory-genomics.org/rgt/basic-introduction/ RGT]
+
|[http://www.biostat.jhsph.edu/~hji/cisgenome/ cisgenome]
−
|0.11.3-IGB-gcc-4.9.4-Python-2.7.13
+
|2.0-IGB-gcc-4.9.4
−
|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.
+
|An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
 
|-
 
|-
−
|[https://github.com/matterport/Mask_RCNN MaskRCNN]
+
|[https://github.com/YeoLab/clipper clipper]
−
|20190227-IGB-gcc-4.9.4-Python-3.6.1
+
|1.2.1-IGB-gcc-4.9.4-Python-2.7.13
−
|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.  
+
|A tool to detect CLIP-seq peaks.
 
|-
 
|-
−
|numactl
+
|[http://clusterflow.io/ clusterflow]
−
|
+
|0.5-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.
+
|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://deeplearning.net/software/libgpuarray/ libgpuarray]
+
|[https://github.com/cocodataset/cocoapi cocoapi]
−
|0.6.5-IGB-gcc-4.9.4
+
|20190218-IGB-gcc-4.9.4-Python-3.6.1
−
|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/
+
|OCO is a large image dataset designed for object detection, segmentation, person keypoints detection, stuff segmentation, and caption generation.
 
|-
 
|-
−
|[https://github.com/stamatak/standard-RAxML RAxML]
+
|[http://www.gnu.org/software/coreutils/coreutils.html coreutils]
−
|8.2.12-IGB-gcc-4.9.4
+
|8.28-IGB-gcc-4.9.4
−
|RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
+
|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.  
 
|-
 
|-
−
|[http://research-pub.gene.com/gmap/ GMAP]
+
|[https://github.com/iqbal-lab/cortex cortex]
−
|2018-05-30-IGB-gcc-4.9.4
+
|1.0.5.21-IGB-gcc-4.9.4
−
|A Genomic Mapping and Alignment Program for mRNA and EST Sequences, andGSNAP: Genomic Short-read Nucleotide Alignment Program
+
|reference free variant assembly
 
|-
 
|-
−
|[https://www.cog-genomics.org/plink2 plink]
+
|[https://github.com/cboursnell/crb-blast crb-blast]
−
|1.07<br>1.90
+
|0.6.9-IGB-gcc-4.9.4
−
|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.  
+
|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://bioinf.uni-greifswald.de/augustus/ AUGUSTUS]
+
|[https://github.com/broadinstitute/cromwell cromwell]
−
|3.3-IGB-gcc-4.9.4
+
|39-Java-1.8.0_152
−
|AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences
+
|Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
 
|-
 
|-
−
|[http://korflab.ucdavis.edu/software.html SNAP]
+
|[https://developer.nvidia.com/cudnn cuDNN]
−
|2013-11-29-IGB-gcc-4.9.4
+
|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-IGB-gcc-4.9.4-CUDA-9.0.176<br>7.1.4-IGB-gcc-4.9.4-CUDA-9.0.176<br>7.6.1.34-CUDA-10.0.130
−
|(Semi-HMM-based Nucleic Acid Parser) gene prediction tool
+
|The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for    deep neural networks.
 
|-
 
|-
−
|[http://ipython.org/index.html IPython]
+
|[http://opensource.scilifelab.se/projects/cutadapt/ cutadapt]
−
|5.3.0-IGB-gcc-4.9.4-Python-3.6.1
+
|1.14-IGB-gcc-4.9.4-Python-2.7.13<br>1.17-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.
+
|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/md5sam/Falcon2Fastg Falcon2Fastg]
+
|[https://cytoscape.org/ cytoscape]
−
|0.3.1-IGB-gcc-4.9.4-Python-2.7.13
+
|3.3.0-Java-1.8.0_152-2.8tb<br>3.3.0-Java-1.8.0_152-350gb<br>3.7.0-Java-1.8.0_152-2.8tb<br>3.7.0-Java-1.8.0_152-350gb
−
|This software converts the results of PacBio assembly using FALCON, to a FASTG graph that can be visualized using Bandage.
+
|Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
 
|-
 
|-
−
|[https://bitbucket.org/feeldead/gfold GFOLD]
+
|[http://owenjm.github.io/damidseq_pipeline/ damidseq]
−
|1.1.4-IGB-gcc-4.9.4
+
|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.
+
|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://jgi.doe.gov/data-and-tools/bbtools/ BBMap]
+
|[https://github.com/fidelram/deepTools deepTools]
−
|38.36-Java-1.8.0_152
+
|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
−
|BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
+
|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.
 
|-
 
|-
−
|[http://www.clustal.org/omega/ Clustal-Omega]
+
|[https://github.com/spragunr/deep_q_rl deep_q_rl]
−
|1.2.4-IGB-gcc-4.9.4
+
|20160603-IGB-gcc-4.9.4-Python-2.7.13
−
|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  - Homepage: http://www.clustal.org/omega/
+
|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.
 
|-
 
|-
−
|[http://www.gnu.org/software/gdb/gdb.html gdb]
+
|[https://github.com/dellytools/delly delly]
−
|8.0.1-IGB-gcc-4.9.4-Python-2.7.13
+
|0.8.1-IGB-gcc-4.9.4
−
|The GNU Project Debugger
+
|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://github.com/Kingsford-Group/rnaseqtools rnaseqtools]
+
|[https://github.com/shenlab-sinai/diffreps diffReps]
−
|1.0.2-IGB-gcc-4.9.4
+
|1.55.6-IGB-gcc-4.9.4-Perl-5.24.1
−
|This repo rnaseqtools provides a set of tools to process transcripts (mainly in gtf format).  
+
|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://www.tensorflow.org/ Tensorflow-GPU]
+
|[http://www.crypticlineage.net/pages/distruct.html distruct]
−
|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
+
|2.2-IGB-gcc-4.9.4
−
|An open-source software library for Machine Intelligence
+
|Modified version of the original distruct.py
 
|-
 
|-
−
|Pango
+
|[http://expressionanalysis.github.io/ea-utils/ ea-utils]
−
|
+
|1.04.807-IGB-gcc-4.9.4
−
|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. - Homepage: http://www.pango.org/
+
|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.
 
|-
 
|-
−
|[https://github.com/wdecoster/nanopack nanopack]
+
|efiest/beta
−
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
+
|beta
−
|Easily install all my long read processing and analysis scripts simultaneously.
+
|
 
|-
 
|-
−
|[http://www.microbesonline.org/fasttree/ FastTree]
+
|efiest/beta_private
−
|2.1.10-IGB-gcc-4.9.4
+
|beta_private
−
|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.
+
|
 
|-
 
|-
−
|[https://github.com/PacificBiosciences/bax2bam bax2bam]
+
|efiest/devel
−
|20171114-IGB-gcc-4.9.4
+
|devel
−
|bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAMbasecall format.
+
|
 
|-
 
|-
−
|libsodium
+
|efiest/devlocal
 +
|devlocal
 
|
 
|
−
|Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
 
 
|-
 
|-
−
|[https://github.com/lh3/miniasm miniasm]
+
|efiest/efitools
−
|0.2-IGB-gcc-4.9.4
+
|efitools/devlocal
−
|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://github.com/DRL/blobtools blobtools]
+
|efiest/prod
−
|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
+
|prod
−
|Application for the visualisation of (draft) genome assemblies using TAGC (Taxon-annotated Gc-Coverage) plots
+
|
 
|-
 
|-
−
|[https://cran.r-project.org/web/packages/Rmpi/index.html Rmpi]
+
|efiest/prod_private
−
|0.6-6-IGB-gcc-4.9.4-R-3.4.2
+
|prod_private
−
|An interface (wrapper) to MPI APIs. It also provides interactive R manager and worker environment.
+
|
 +
|-
 +
|[https://github.com/DReichLab/EIG 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).  
 
|-
 
|-
−
|[http://ghostscript.com GhostScript]
+
|[https://github.com/biocore-ntnu/epic epic]
−
|9.21-IGB-gcc-4.9.4
+
|0.2.9-IGB-gcc-4.9.4-Python-2.7.13
−
|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. - Homepage: http://ghostscript.com
+
|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/STAR-Fusion/STAR-Fusion/wiki STAR-Fusion]
+
|[https://github.com/biocore-ntnu/epic2 epic2]
−
|1.6.0-IGB-gcc-4.9.4
+
|0.0.41-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use.
 
|-
 
|-
−
|[http://jupyter.org/ jupyterlab]
+
|[https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate exonerate]
−
|0.34.10-IGB-gcc-4.9.4-Python-3.6.1<br>0.35.6-IGB-gcc-4.9.4-Python-3.6.1<br>1.0.4-IGB-gcc-4.9.4-Python-3.6.1
+
|2.2.0-IGB-gcc-4.9.4
−
|Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages.
+
|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.
 
|-
 
|-
−
|Tk
+
|expat
 
|
 
|
−
|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.
+
|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)
 
|-
 
|-
−
|libpng
+
|[https://github.com/mateidavid/fast5 fast5]
−
|
+
|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
−
|libpng is the official PNG reference library
+
|A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
−
|-
 
−
|singularity
 
−
|3.4.1
 
−
|Application and environment virtualization
 
 
|-
 
|-
 
|[http://scheet.org/software.html fastPHASE]
 
|[http://scheet.org/software.html fastPHASE]
Line 1,537: Line 1,577:
 
|astPHASE is a program to estimate missing genotypes and unobserved haplotypes.  
 
|astPHASE is a program to estimate missing genotypes and unobserved haplotypes.  
 
|-
 
|-
−
|[https://github.com/kundajelab/phantompeakqualtools Phantompeaktools]
+
|[https://github.com/OpenGene/fastp fastp]
−
|1.2-IGB-gcc-4.9.4-R-3.4.1
+
|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
−
|Custom SPP for Phantompeaktools
+
|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.
 
|-
 
|-
−
|[https://github.com/google/protobuf protobuf]
+
|[https://github.com/adrianlopezroche/fdupes fdupes]
−
|2.6.1-IGB-gcc-4.9.4<br>3.5.0-IGB-gcc-4.9.4
+
|1.6.1-IGB-gcc-4.9.4
−
|Protocol Buffers (a.k.a., protobuf) are Googles language-neutral, platform-neutral, extensible mechanism for serializing structured data.
+
|FDUPES is a program for identifying duplicate files residingwithin specified directories.
 
|-
 
|-
−
|[https://github.com/spragunr/deep_q_rl deep_q_rl]
+
|[http://fulcrumgenomics.github.io/fgbio/ fgbio]
−
|20160603-IGB-gcc-4.9.4-Python-2.7.13
+
|0.6.0-Java-1.8.0_152
−
|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.
+
|fgbio is a command line toolkit for working with genomic and particularly next generation sequencing data.
 
|-
 
|-
−
|[http://www.nwchem-sw.org NWChem]
+
|file
−
|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.
+
|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.
 
|-
 
|-
−
|ncurses
+
|flex
 
|
 
|
−
|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.
+
|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/ruanjue/wtdbg2 wtdbg2]
+
|[https://github.com/seqan/flexbar flexbar]
−
|2.3-IGB-gcc-4.9.4
+
|3.0.3-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.
+
|The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided.  
 
|-
 
|-
−
|[http://www.htslib.org/ SAMtools]
+
|fontconfig
−
|0.1.20-IGB-gcc-4.9.4<br>1.10-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
+
|
−
|SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
+
|Fontconfig is a library designed to provide system-wide font configuration, customization andapplication access.
 
|-
 
|-
−
|[https://sourceforge.net/projects/phispy PhiSpy]
+
|[https://github.com/Discngine/fpocket fpocket]
−
|2.3-IGB-gcc-4.9.4-Python-2.7.13
+
|3.1.3-IGB-gcc-4.9.4
−
|A novel algorithm for finding prophages in microbial genomes that combines similarity-based and composition-based strategies
+
|fpocket is a very fast open source protein pocket detection algorithm based on Voronoi tessellation.
 
|-
 
|-
−
|[http://www.digip.org/jansson/ jansson]
+
|freetype
−
|2.6-IGB-gcc-4.9.4
+
|
−
|Jansson is a C library for encoding, decoding and manipulating JSON data.  
+
|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.
 
|-
 
|-
−
|[https://github.com/iqbal-lab/cortex cortex]
+
|[http://www.gnu.org/software/gdb/gdb.html gdb]
−
|1.0.5.21-IGB-gcc-4.9.4
+
|8.0.1-IGB-gcc-4.9.4-Python-2.7.13
−
|reference free variant assembly
+
|The GNU Project Debugger
 
|-
 
|-
−
|[http://www.repeatmasker.org/ RepeatMasker]
+
|[https://gdc.cancer.gov/access-data/gdc-data-transfer-tool gdc-client]
−
|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
+
|1.3.0-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.  
+
|The GDC Data Transfer Tool Client provides a command-line interface supporting both GDC data downloads and submissions.
 
|-
 
|-
−
|[http://bazel.io/ bazel]
+
|[http://www1.montpellier.inra.fr/CBGP/software/GeneClass/ geneclass]
−
|0.6.0-Java-1.8.0_121
+
|2.0
−
|Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Googles software.
+
|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.
 
|-
 
|-
−
|[http://www.graphicsmagick.org/ GraphicsMagick]
+
|gengetopt
−
|1.3.26-IGB-gcc-4.9.4
+
|
−
|GraphicsMagick is the swiss army knife of image processing.
+
|Gengetopt is a tool to write command line option parsing code for C programs. - Homepage: https://www.gnu.org/software/gengetopt/gengetopt.html
 
|-
 
|-
−
|[https://github.com/IGBIllinois/biodatabase/ biodatabase]
+
|[http://genometools.org/ genometools]
−
|1.0-IGB-gcc-4.9.4
+
|1.5.10-IGB-gcc-4.9.4
−
|Scripts to create databases on the biodatabase machine.
+
|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.
 
|-
 
|-
−
|[http://www1.montpellier.inra.fr/CBGP/diyabc/index.php DIYABC]
+
|[http://trac.osgeo.org/geos geos]
−
|2.1.0
+
|3.7.1-IGB-gcc-4.9.4
−
|a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers
+
|GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite
 
|-
 
|-
−
|[https://symas.com/lmdb LMDB]
+
|gettext
−
|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.
+
|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
 
|-
 
|-
−
|[https://github.com/andyrimmer/Platypus Platypus]
+
|[http://acgt.cs.tau.ac.il/gevalt/ gevalt]
−
|20180622-IGB-gcc-4.9.4-Python-2.7.13
+
|2.0-Java-1.8.0_152
−
|The Platypus variant caller.  
+
|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/chanzuckerberg/shasta shasta]
+
|[http://ccb.jhu.edu/software/stringtie/gffcompare.shtml gffcompare]
−
|0.2.0
+
|0.10.6-IGB-gcc-4.9.4
−
|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.
+
|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).  
 
|-
 
|-
−
|[https://github.com/torch/distro Torch]
+
|[http://ccb.jhu.edu/software/stringtie/gff.shtml gffread]
−
|20171018-IGB-gcc-4.9.4-Python-3.6.1
+
|ba7535f-IGB-gcc-4.9.4
−
|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.
+
|The program gffread can be used to validate, filter, convert and perform various other operations on GFF files
 
|-
 
|-
−
|[https://github.com/TransDecoder/TransDecoder/wiki TransDecoder]
+
|[http://git-scm.com/ git]
−
|5.1.0-IGB-gcc-4.9.4-Perl-5.24.1
+
|2.9.5-IGB-gcc-4.9.4
−
|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.
+
|Git is a free and open source distributed version control system designedto handle everything from small to very large projects with speed and efficiency.
 
|-
 
|-
−
|[http://ab.inf.uni-tuebingen.de/software/megan6/ MEGAN]
+
|[https://git-lfs.github.com/ git-lfs]
−
|6.12.2-Java-1.8.0_152
+
|2.2.1-IGB-gcc-4.9.4
−
|MEGAN6 is a comprehensive toolbox for interactively analyzing microbiome data. All the interactive tools you need in one application.
+
|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://ccb.jhu.edu/software/tophat/index.shtml TopHat]
+
|glproto
−
|1.4.1<br>2.1.1-IGB-gcc-4.9.4
+
|
−
|TopHat is a fast splice junction mapper for RNA-Seq reads.
+
|X protocol and ancillary headers
 
|-
 
|-
−
|[https://bitbucket.org/biobakery/kneaddata/wiki/Home KneadData]
+
|[http://gnuplot.sourceforge.net/ gnuplot]
−
|0.6.1-IGB-gcc-4.9.4-Python-3.6.1
+
|4.6.7-IGB-gcc-4.9.4<br>5.0.6-IGB-gcc-4.9.4
−
|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.
+
|Portable interactive, function plotting utility - Homepage: http://gnuplot.sourceforge.net/
 
|-
 
|-
−
|[https://metavelvet.dna.bio.keio.ac.jp/ MetaVelvet]
+
|gompi
−
|1.2.02-IGB-gcc-4.9.4
+
|
−
|An extension of Velvet assembler to de novo metagenome assembly from short sequence reads
+
|GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
 
|-
 
|-
−
|[https://github.com/lmrodriguezr/rocker bio-rocker]
+
|[https://github.com/data61/gossamer gossamer]
−
|1.2.0-IGB-gcc-4.9.4-Ruby-2.4.2
+
|20170105-IGB-gcc-4.9.4
−
|Accurately detecting functional genes in metagenomes.
+
|The gossamer bioinformatics suite contains goss, gossple, xenome, and electus
 
|-
 
|-
−
|[http://pandoc.org pandoc]
+
|[https://www.gnu.org/software/gperf/ gperf]
−
|2.2.3.2
+
|3.1-IGB-gcc-4.9.4
−
|If you need to convert files from one markup format into another, pandoc is your swiss-army knife
+
|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.
 
|-
 
|-
−
|[http://computation.llnl.gov/projects/sundials SUNDIALS]
+
|[https://bitbucket.org/nsegata/graphlan/ graphlan]
−
|2.6.2-IGB-gcc-4.9.4
+
|6ca8735-IGB-gcc-4.9.4-Python-2.7.13
−
|SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
+
|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://bitbucket.org/berkeleylab/metabat MetaBAT]
+
|[https://github.com/DecodeGenetics/graphtyper graphtyper]
−
|2.12.1
+
|1.3-IGB-gcc-4.9.4
−
|MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
+
|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.
 
|-
 
|-
−
|shortbred/prod
+
|[http://www.graphviz.org/ graphviz]
−
|prod
+
|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.
 
|-
 
|-
−
|[http://sanger-pathogens.github.io/circlator/ Circlator]
+
|[https://github.com/google/googletest gtest]
−
|1.5.1-IGB-gcc-4.9.4-Python-3.6.1
+
|1.8.0-IGB-gcc-4.9.4
−
|A tool to circularize genome assemblies.
+
|Googles C++ test framework
 
|-
 
|-
−
|[https://www.pacb.com/support/software-downloads/ smrtlink]
+
|[http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html gtool]
−
|8.0.0.80529
+
|0.7.5
−
|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.
+
|GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.  
 
|-
 
|-
−
|[https://github.com/kblin/ncbi-genome-download ncbi-genome-download]
+
|[https://community.nanoporetech.com/posts/pre-release-of-stand-alone guppy]
−
|0.2.9-IGB-gcc-4.9.4-Python-3.6.1
+
|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
−
|Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago.
+
|Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.  
 
|-
 
|-
−
|[http://emboss.sourceforge.net/ EMBOSS]
+
|[https://community.nanoporetech.com/posts/pre-release-of-stand-alone guppy-gpu]
−
|6.6.0-IGB-gcc-4.9.4-Java-1.8.0_121
+
|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>3.4.5
−
|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.
+
|Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.  
 
|-
 
|-
−
|[https://github.com/Generade-nl/TULIP TULIP]
+
|[https://cran.r-project.org/web/packages/h2o/index.html h2o]
−
|20170513-IGB-gcc-4.9.4-Perl-5.24.1
+
|3.14.0.3-IGB-gcc-4.9.4-R-3.3.3
−
|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.
+
|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.
 
|-
 
|-
−
|[https://nanoporetech.com/ albacore]
+
|h5py
−
|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
+
|The h5py package provides both a high- and low-level interface to the HDF5 library from Python.
 
|-
 
|-
−
|[http://blast.ncbi.nlm.nih.gov/ BLAST+]
+
|[https://forge-dga.jouy.inra.fr/projects/hapflk hapflk]
−
|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
+
|1.4-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|hapflk is a software implementing the hapFLK and FLK tests for the detection of selection signatures based on multiple population genotyping data.
 
|-
 
|-
−
|[https://ninja-build.org/ ninja]
+
|help2man
−
|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.
 
−
|-
 
−
|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.
+
|help2man produces simple manual pages from the --help and --version output of other commands.
 
|-
 
|-
−
|[https://www.mathworks.com/help/matlab/matlab-engine-for-python.html MATLAB-python]
+
|[https://github.com/soedinglab/hh-suite hhsuite]
−
|2017b-IGB-gcc-4.9.4-Python-3.6.1
+
|3.2.0
−
|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.
+
|The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models
 
|-
 
|-
−
|Autotools
+
|hwloc
 
|
 
|
−
|This bundle collect the standard GNU build tools: Autoconf, Automake and libtool
+
|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://acgt.cs.tau.ac.il/gevalt/ gevalt]
+
|[http://icorn.sourceforge.net/documentation.html icorn]
−
|2.0-Java-1.8.0_152
+
|0.97-IGB-gcc-4.9.4
−
|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.
+
|Inputs: Reference Sequence (FASTA) & reads (FASTQ) & information of short reads
 
|-
 
|-
−
|[https://github.com/tseemann/prokka prokka]
+
|[http://software.broadinstitute.org/software/igv/ igv]
−
|1.13-IGB-gcc-4.9.4-Perl-5.24.1<br>1.14.6-IGB-gcc-4.9.4-Perl-5.24.1
+
|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
−
|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.
+
|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://github.com/luntergroup/octopus octopus]
+
|[https://mathgen.stats.ox.ac.uk/impute/impute_v2.html impute2]
−
|0.6.3-beta-IGB-gcc-8.2.0
+
|2.3.2
−
|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.  
+
|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.  
 
|-
 
|-
−
|Tcl
+
|[https://github.com/LLNL/ior ior]
−
|
+
|3.0.1-IGB-gcc-4.9.4
−
|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.
+
|Parallel filesystem I/O benchmark
 
|-
 
|-
−
|[http://rna.urmc.rochester.edu/RNAstructure.html RNAstructure]
+
|[http://www.digip.org/jansson/ jansson]
−
|6.0-IGB-gcc-4.9.4
+
|2.6-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.  
+
|Jansson is a C library for encoding, decoding and manipulating JSON data.  
 
|-
 
|-
−
|[https://github.com/ncbi/ngs NGS]
+
|[http://www.canonware.com/jemalloc jemalloc]
−
|1.3.0-IGB-gcc-4.9.4
+
|5.0.1-IGB-gcc-4.9.4
−
|NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. - Homepage: https://github.com/ncbi/ngs
+
|jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
 
|-
 
|-
−
|[http://cab.spbu.ru/software/spades/ SPAdes]
+
|[http://jupyter.org/ jupyter]
−
|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
+
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
−
|SPAdes . St. Petersburg genome assembler . is intended for both standard isolates and single-cell MDA bacteria assemblies.
+
|Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages.
 
|-
 
|-
−
|[http://picrust.github.io/picrust/ PICRUSt]
+
|[http://jupyter.org/ jupyterlab]
−
|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
+
|0.34.10-IGB-gcc-4.9.4-Python-3.6.1<br>0.35.6-IGB-gcc-4.9.4-Python-3.6.1<br>1.0.4-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|Project Jupyter exists to develop open-source software, open-standards, and services for interactive computing across dozens of programming languages.
 
|-
 
|-
−
|[https://root.cern.ch/ root]
+
|[http://pachterlab.github.io/kallisto/ kallisto]
−
|6.14.06-IGB-gcc-4.9.4
+
|0.43.1-IGB-gcc-4.9.4<br>0.44.0-IGB-gcc-4.9.4
−
|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.
+
|kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
 
|-
 
|-
−
|libtool
+
|[http://genome.cse.ucsc.edu kentUtils]
−
|
+
|353-IGB-gcc-4.9.4
−
|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
+
|UCSC genome browser kent bioinformatic utilities
 
|-
 
|-
−
|[http://opensource.scilifelab.se/projects/cutadapt/ cutadapt]
+
|[https://github.com/matthiasplappert/keras-rl keras-rl]
−
|1.14-IGB-gcc-4.9.4-Python-2.7.13<br>1.17-IGB-gcc-4.9.4-Python-3.6.1
+
|0.3.0-IGB-gcc-4.9.4-Python-2.7.13
−
|Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.  
+
|keras-rl implements some state-of-the art deep reinforcement learning algorithms in Python and seamlessly integrates with the deep learning library Keras.  
 
|-
 
|-
−
|[https://github.com/mcveanlab/mccortex McCortex]
+
|[https://github.com/alticelabs/kyoto kyoto]
−
|1.0.1-IGB-gcc-4.9.4
+
|20170410-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.
+
|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://www.sqlite.org/ SQLite]
+
|[http://lbzip2.org/ lbzip2]
−
|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
+
|2.5-IGB-gcc-4.9.4
−
|SQLite: SQL Database Engine in a C Library
+
|lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format.
 
|-
 
|-
−
|[http://www.mathworks.com/products/matlab MATLAB]
+
|[https://lftp.yar.ru/ lftp]
−
|2017a<br>2017b
+
|4.8.3
−
|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.
+
|FTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).  
 
|-
 
|-
−
|[http://www.bcgsc.ca/platform/bioinfo/software/links LINKS]
+
|libcerf
−
|1.8.5-IGB-gcc-4.9.4-Perl-5.24.1
+
|
−
|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).
+
|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/COMBINE-lab/salmon Salmon]
+
|libdap
−
|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
+
|
−
|Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
+
|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.
 
|-
 
|-
−
|[https://github.com/aidenlab/juicer Juicer]
+
|libdrm
−
|1.13.02-Java-1.8.0_152
+
|
−
|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.
+
|Direct Rendering Manager runtime library.
 
|-
 
|-
−
|[https://github.com/smirarab/sepp SEPP]
+
|libevent
−
|20180223-IGB-gcc-4.9.4-Python-2.7.13
+
|
−
|SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
+
|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://subread.sourceforge.net/ Subread]
+
|libffi
−
|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
+
|
−
|High performance read alignment, quantification and mutation discovery
+
|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://smithlabresearch.org/software/preseq/ preseq]
+
|libgd
−
|2.0.3-IGB-gcc-4.9.4
+
|
−
|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.
+
|GD is an open source code library for the dynamic creation of images by programmers. - Homepage: http://libgd.bitbucket.org/
 
|-
 
|-
−
|Autoconf
+
|libgdiplus
 
|
 
|
−
|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/
+
|An Open Source implementation of the GDI+ API
 
|-
 
|-
−
|[https://github.com/velocyto-team/velocyto.R velocyto.R]
+
|[http://deeplearning.net/software/libgpuarray/ libgpuarray]
−
|20190527-IGB-gcc-4.9.4-R-3.4.2
+
|0.6.5-IGB-gcc-4.9.4
−
|RNA velocity estimation in R
+
|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/
 
|-
 
|-
−
|[https://github.com/pysam-developers/pysam Pysam]
+
|libgtextutils
−
|0.13.0-IGB-gcc-4.9.4-Python-2.7.13<br>0.13.0-IGB-gcc-4.9.4-Python-3.6.1
+
|
−
|Pysam is a python module for reading and manipulating Samfiles.  Its a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
+
|ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream - Homepage: http://hannonlab.cshl.edu/fastx_toolkit/
 
|-
 
|-
−
|[http://www.genome.umd.edu/jellyfish.html Jellyfish]
+
|[http://libharu.org/ libharu]
−
|1.1.12-IGB-gcc-4.9.4<br>2.2.10-IGB-gcc-8.2.0<br>2.2.6-IGB-gcc-4.9.4
+
|2.3.0-IGB-gcc-4.9.4
−
|Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
+
|libHaru is a free, cross platform, open source library for generating PDF files. - Homepage: http://libharu.org/
 
|-
 
|-
−
|[http://www.bioinformatics.babraham.ac.uk/projects/bismark/ Bismark]
+
|libjpeg-turbo
−
|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
+
|
−
|A tool to map bisulfite converted sequence reads and determine cytosine methylation states
+
|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.
 
|-
 
|-
−
|[https://aws.amazon.com/cli/ awscli]
+
|libpciaccess
−
|1.16.113-IGB-gcc-4.9.4-Python-3.6.1
+
|
−
|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.
+
|Generic PCI access library.
 
|-
 
|-
−
|[http://sourceforge.net/projects/snpeff/ snpEff]
+
|libpng
−
|4.3o-Java-1.8.0_121<br>4.3t-Java-1.8.0_152
+
|
−
|SnpEff is a variant annotation and effect prediction tool.  It annotates and predicts the effects of genetic variants (such as amino acid changes).
+
|libpng is the official PNG reference library
 
|-
 
|-
−
|[http://www.r-project.org/ R]
+
|libpthread-stubs
−
|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
+
|
−
|R is a free software environment for statistical computing and graphics.
+
|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.
 
|-
 
|-
−
|[https://github.com/IGBIllinois/memprof memprof]
+
|libreadline
−
|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.
+
|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.
 
|-
 
|-
−
|[http://smithlabresearch.org/software/piranha/ piranha]
+
|libsodium
−
|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.  
+
|Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.
 
|-
 
|-
−
|[http://merenlab.org/software/anvio/ anvio]
+
|libtool
−
|5.5-IGB-gcc-4.9.4-Python-3.6.1<br>6.1-IGB-gcc-4.9.4-Python-3.6.1
+
|
−
|Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.
+
|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://github.com/nanoporetech/medaka medaka]
+
|libxml2
−
|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.
+
|Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).
 
|-
 
|-
−
|[http://eddylab.org/software/recon/ RECON]
+
|libxslt
−
|1.08-IGB-gcc-4.9.4-Perl-5.24.1
+
|
−
|a package for automated de novo identification of repeat families from genomic sequences
+
|Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
 
|-
 
|-
−
|[http://www.meilerlab.org/index.php/bclcommons/show/b_apps_id/1 bcl]
+
|[http://support.10xgenomics.com/genome-exome/software/pipelines/latest/what-is-long-ranger longranger]
−
|4.0.0
+
|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
 
|-
 
|-
−
|[https://www.mdc-berlin.de/8551903/en/ mirdeep]
+
|[https://support.10xgenomics.com/genome-exome/software/visualization/latest/what-is-loupe loupe]
−
|2.0.0.8-IGB-gcc-4.9.4
+
|2.1.1
−
|miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.  
+
|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.
 
|-
 
|-
−
|gettext
+
|[https://sourceforge.net/projects/lpsolve/ lpsolve]
−
|
+
|5.5.2.5-IGB-gcc-4.9.4
−
|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
+
|Mixed Integer Linear Programming (MILP) solver
 
|-
 
|-
−
|[http://www-huber.embl.de/users/anders/HTSeq/ HTSeq]
+
|[https://github.com/arq5x/lumpy-sv lumpy]
−
|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
+
|0.3.0-IGB-gcc-4.9.4
−
|A framework to process and analyze data from high-throughput sequencing (HTS) assays
+
|A probabilistic framework for structural variant discovery.
 
|-
 
|-
−
|[http://www.scons.org/ SCons]
+
|lzo
−
|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.
+
|Portable lossless data compression library
 
|-
 
|-
−
|[https://developer.gnome.org/gtk+/stable/ GTK+]
+
|[https://bitbucket.org/liulab/mageck-vispr mageck-vispr]
−
|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
+
|0.5.4-IGB-gcc-4.9.4-Python-3.6.1
−
|The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
+
|MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens.
 
|-
 
|-
−
|tbb
+
|[https://github.com/DpeerLab/magic magic]
−
|
+
|0.1-IGB-gcc-4.9.4-Python-3.6.1<br>0.1.1-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|A diffusion-based imputation method reveals gene-gene interactions in single-cell RNA-sequencing data
 
|-
 
|-
−
|[https://github.com/bcgsc/arcs ARCS]
+
|[https://github.com/ginolhac/mapDamage mapDamage]
−
|1.0.0-IGB-gcc-4.9.4-Perl-5.24.1
+
|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
−
|Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. - Homepage: https://github.com/bcgsc/arcs
+
|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://git.wageningenur.nl/medema-group/BiG-SCAPE BiG-SCAPE]
+
|[https://github.com/nanoporetech/medaka medaka]
−
|20181115-IGB-gcc-4.9.4-Python-3.6.1
+
|0.1.0-IGB-gcc-4.9.4-Python-3.6.1
−
|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)
+
|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.
−
|-
 
−
|[http://www.numpy.org numpy]
 
−
|1.14.1-IGB-gcc-4.9.4-Python-3.6.1
 
−
|NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be  defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
 
 
|-
 
|-
−
|[https://www.seqan.de/ seqan]
+
|[https://github.com/nanoporetech/megalodon/ megalodon]
−
|2.3.2-IGB-gcc-4.9.4
+
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
−
|SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data
+
|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.
 
|-
 
|-
−
|[https://github.com/biocore-ntnu/epic2 epic2]
+
|[https://github.com/IGBIllinois/memprof memprof]
−
|0.0.41-IGB-gcc-4.9.4-Python-3.6.1
+
|1.01
−
|epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use.
+
|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://github.com/arq5x/lumpy-sv lumpy]
+
|[https://bitbucket.org/biobakery/metaphlan2 metaphlan2]
−
|0.3.0-IGB-gcc-4.9.4
+
|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
−
|A probabilistic framework for structural variant discovery.
+
|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.
 
|-
 
|-
−
|Clp
+
|[https://www.agisoft.com/ metashape]
−
|
+
|1.5.1-IGB-gcc-4.9.4
−
|Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.  
+
|photogrammetricprocessing of digital images and 3D spatial data generation
 
|-
 
|-
−
|[http://weizhong-lab.ucsd.edu/cd-hit/ CD-HIT]
+
|[https://github.com/LangilleLab/microbiome_helper microbiome_helper]
−
|4.6.6-IGB-gcc-4.9.4
+
|20171114-IGB-gcc-4.9.4
−
|CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. - Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
+
|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.
 
|-
 
|-
−
|[https://gradle.org Gradle]
+
|[http://microbiomeutil.sourceforge.net/ microbiomeutil]
−
|4.7
+
|20110519-IGB-gcc-4.9.4
−
|Complete Gradle install.From mobile apps to microservices, from small startups to big enterprises,Gradle helps teams build, automate and deliver better software, faster.
+
|Contains ChimeraSlayer, WigeoN, and NAST-iEr
 
|-
 
|-
−
|ANTLR
+
|[https://github.com/lh3/miniasm miniasm]
−
|
+
|0.2-IGB-gcc-4.9.4
−
|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.
+
|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.
 
|-
 
|-
−
|[http://www.cbs.dtu.dk/cgi-bin/sw_request?rnammer RNAmmer]
+
|[https://github.com/lh3/minimap minimap]
−
|1.2-IGB-gcc-4.9.4-Perl-5.24.1
+
|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>2.3-IGB-gcc-4.9.4<br>2.8-IGB-gcc-4.9.4
−
|Ribosomal RNA sub units
+
|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://abacus.gene.ucl.ac.uk/software/paml.html PAML]
+
|[https://github.com/PacificBiosciences/minorseq/blob/54ac795d7c119d21a4611d91ac458cd3e2e2b30a/doc/INSTALL.md minorseq]
−
|4.9e-IGB-gcc-4.9.4
+
|20180314-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
+
|Minor Variant Calling and Phasing Tools
 
|-
 
|-
−
|[http://fenderglass.github.io/Ragout/ Ragout]
+
|[https://www.mdc-berlin.de/8551903/en/ mirdeep]
−
|2.0-IGB-gcc-4.9.4
+
|2.0.0.8-IGB-gcc-4.9.4
−
|Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references.  
+
|miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.  
 
|-
 
|-
−
|[https://github.com/ruanjue/smartdenovo SMARTdenovo]
+
|[https://github.com/wdecoster/nanopack nanopack]
−
|20170916-IGB-gcc-4.9.4-Perl-5.24.1
+
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|Easily install all my long read processing and analysis scripts simultaneously.
 
|-
 
|-
−
|[https://support.10xgenomics.com/single-cell-atac/software/pipelines/latest/what-is-cell-ranger-atac cellranger-atac]
+
|[https://github.com/jts/nanopolish nanopolish]
−
|1.1.0
+
|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>0.6.0-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
−
|Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data.  
+
|Software package for signal-level analysis of Oxford Nanopore sequencing data.
 
|-
 
|-
−
|[http://www1.montpellier.inra.fr/CBGP/software/GeneClass/ geneclass]
+
|[https://github.com/kblin/ncbi-genome-download ncbi-genome-download]
−
|2.0
+
|0.2.9-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|Some script to download bacterial and fungal genomes from NCBI after they restructured their FTP a while ago.
 
|-
 
|-
−
|[https://github.com/marbl/Krona Krona]
+
|[https://github.com/ncbi/ncbi-vdb ncbi-vdb]
−
|2.7-IGB-gcc-4.9.4-Perl-5.24.1
+
|2.8.2-IGB-gcc-4.9.4
−
|Interactively explore metagenomes and more from a web browser.
+
|The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. - Homepage: https://github.com/ncbi/ncbi-vdb
 
|-
 
|-
−
|[http://drive5.com/muscle/ MUSCLE]
+
|[http://cran.r-project.org/web/packages/ncdf4 ncdf4]
−
|3.8.31-IGB-gcc-4.9.4
+
|1.16-IGB-gcc-4.9.4-R-3.3.3
−
|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/
+
|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.
 
|-
 
|-
−
|[https://github.com/soedinglab/MMseqs2 MMseqs2]
+
|ncurses
−
|10-6d92c
+
|
−
|MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.  
+
|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://icorn.sourceforge.net/documentation.html icorn]
+
|[http://www.unidata.ucar.edu/software/netcdf/ netCDF]
−
|0.97-IGB-gcc-4.9.4
+
|4.4.1.1-IGB-gcc-4.9.4<br>4.7.2-IGB-gcc-8.2.0
−
|Inputs: Reference Sequence (FASTA) & reads (FASTQ) & information of short reads
+
|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://ccb.jhu.edu/software/stringtie/ StringTie]
+
|[http://www.unidata.ucar.edu/software/netcdf/ netCDF-Fortran]
−
|1.3.3-IGB-gcc-4.9.4<br>1.3.6-IGB-gcc-4.9.4
+
|4.4.1-IGB-gcc-4.9.4
−
|StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
+
|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://mathgen.stats.ox.ac.uk/impute/impute_v2.html impute2]
+
|[http://www.lysator.liu.se/~nisse/nettle/ nettle]
−
|2.3.2
+
|3.3-IGB-gcc-4.9.4
−
|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.  
+
|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.
 
|-
 
|-
−
|[https://github.com/OpenGene/fastp fastp]
+
|[https://www.nextflow.io/ nextflow]
−
|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
+
|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
−
|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.
+
|Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.  
 
|-
 
|-
−
|[https://github.com/rhuebler/HOPS HOPS]
+
|[https://github.com/nf-core/tools nf-core]
−
|0.33
+
|1.6-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|A python package with helper tools for the nf-core community.
 
|-
 
|-
−
|Szip
+
|[https://ninja-build.org/ ninja]
−
|
+
|1.8.2-IGB-gcc-4.9.4
−
|Szip compression software, providing lossless compression of scientific data
+
|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.
 
|-
 
|-
−
|[https://ccb.jhu.edu/software/glimmerhmm GlimmerHMM]
+
|[http://nodejs.org nodejs]
−
|3.0.4-IGB-gcc-4.9.4
+
|10.16.2-IGB-gcc-4.9.4<br>9.9.0-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.
+
|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.
 +
|-
 +
|[http://github.com/wolever/nose-parameterized nose-parameterized]
 +
|0.6.0-IGB-gcc-4.9.4-Python-2.7.13
 +
|Parameterized testing with any Python test framework.
 
|-
 
|-
−
|[http://pachterlab.github.io/kallisto/ kallisto]
+
|[http://www.novocraft.com/ novocraft]
−
|0.43.1-IGB-gcc-4.9.4<br>0.44.0-IGB-gcc-4.9.4
+
|3.08.00
−
|kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
+
|Powerful tool designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, and 454 NGS platforms.
 
|-
 
|-
−
|GCC
+
|numactl
 
|
 
|
−
|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,...).
+
|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://tandem.bu.edu/trf/trf.html trf]
+
|[http://numba.pydata.org/ numba]
−
|4.0.9
+
|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
−
|Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.  
+
|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.
 
|-
 
|-
−
|[https://ccb.jhu.edu/software/centrifuge/ centrifuge]
+
|[http://www.numpy.org numpy]
−
|1.0.3-beta-IGB-gcc-4.9.4<br>1.0.4-beta-IGB-gcc-4.9.4
+
|1.14.1-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be  defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
 
|-
 
|-
−
|[https://github.com/gpertea/cdbfasta cdbfasta]
+
|[https://github.com/luntergroup/octopus octopus]
−
|20170316-IGB-gcc-4.9.4
+
|0.6.3-beta-IGB-gcc-8.2.0
−
|CDB (Constant DataBase) indexing and retrieval tools for FASTA files
+
|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.
 
|-
 
|-
−
|[http://faculty.cse.tamu.edu/davis/suitesparse.html SuiteSparse]
+
|[https://github.com/mirnylab/pairtools pairtools]
−
|5.4.0-IGB-gcc-4.9.4-METIS-5.1.0
+
|0.3.0-IGB-gcc-4.9.4-Python-3.6.1
−
|SuiteSparse is a collection of libraries manipulate sparse matrices.
+
|pairtools is a simple and fast command-line framework to process sequencing data from a Hi-C experiment.
 
|-
 
|-
−
|[http://bowtie-bio.sourceforge.net/index.shtml Bowtie]
+
|[http://www.bork.embl.de/pal2nal/ pal2nal]
−
|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
+
|14-IGB-gcc-4.9.4
−
|Bowtie is an ultrafast, memory-efficient short read aligner.It aligns short DNA sequences (reads) to the human genome.
+
|PAL2NAL is a program that converts a multiple sequence alignment of proteins and the corresponding DNA (or mRNA) sequences into a codon alignment.
 
|-
 
|-
−
|[http://catchenlab.life.illinois.edu/radinitio/ radinitio]
+
|[http://pandoc.org pandoc]
−
|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
+
|2.2.3.2
−
|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.
+
|If you need to convert files from one markup format into another, pandoc is your swiss-army knife
 
|-
 
|-
−
|[https://github.com/lanpa/tensorboardX tensorboardX]
+
|[https://www.gnu.org/software/parallel/ parallel]
−
|1.9-IGB-gcc-4.9.4-Python-3.6.1
+
|20170622-IGB-gcc-4.9.4
−
|TensorBoardX lets you watch Tensors Flow without Tensorflow
+
|parallel: GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
 
|-
 
|-
−
|[http://llvm.org/ LLVM]
+
|[https://github.com/PacificBiosciences/pb-assembly pb-assembly]
−
|4.0.1-IGB-gcc-4.9.4<br>6.0.0-IGB-gcc-4.9.4
+
|0.0.6
−
|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.
+
|PacBio Assembly Tool Suite
 
|-
 
|-
−
|[http://atactk.readthedocs.io/ atactk]
+
|[https://github.com/PacificBiosciences/pbbam pbbam]
−
|0.1.6-IGB-gcc-4.9.4-Python-2.7.13
+
|1.0.7-IGB-gcc-8.2.0
−
|a toolkit for ATAC-seq data
+
|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://www.sanger.ac.uk/science/tools/reapr REAPR]
+
|[https://github.com/PacificBiosciences/ccs pbccs]
−
|1.0.18-IGB-gcc-4.9.4
+
|4.0
−
|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
+
|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://www.crypticlineage.net/pages/software.html strauto]
+
|[http://compression.ca/pbzip2/ pbzip2]
−
|1-IGB-gcc-4.9.4
+
|1.1.13-IGB-gcc-4.9.4
−
|Automation and Parallelization of STRUCTURE Analysis
+
|PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines.
 
|-
 
|-
−
|[http://easybuilders.github.com/easybuild/ EasyBuild]
+
|[http://perfsuite.ncsa.illinois.edu/ perfsuite]
−
|3.5.3<br>3.6.0<br>3.6.2<br>3.9.3
+
|1.1.4-IGB-gcc-4.9.4
−
|EasyBuild is a software build and installation frameworkwritten in Python that allows you to install software in a structured,repeatable and robust way.
+
|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).  
 
|-
 
|-
−
|[https://sourceforge.net/projects/lpsolve/ lpsolve]
+
|[ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/README pfamscan]
−
|5.5.2.5-IGB-gcc-4.9.4
+
|1.6-IGB-gcc-4.9.4-Perl-5.24.1
−
|Mixed Integer Linear Programming (MILP) solver
+
|This readme should help you get started with "pfam_scan.pl", which is for usewith the HMMER3 version of HMMER.
 
|-
 
|-
−
|Eigen
+
|[https://github.com/pgmpy/pgmpy pgmpy]
−
|
+
|20180320-IGB-gcc-4.9.4-Python-3.6.1
−
|Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
+
|pgmpy is a python library for working with Probabilistic Graphical Models.
 
|-
 
|-
−
|[https://github.com/fchollet/keras Keras]
+
|[https://github.com/HRGV/phyloFlash phyloFlash]
−
|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>2.2.0-IGB-gcc-4.9.4-Python-3.6.1<br>2.2.4-IGB-gcc-4.9.4-Python-3.6.1
+
|3.3-IGB-gcc-4.9.4
−
|Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.  
+
|phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset.
 
|-
 
|-
−
|[http://assemblytics.com/ Assemblytics]
+
|[https://bitbucket.org/nsegata/phylophlan/wiki/phylophlan2 phylophlan2]
−
|3f570cd-IGB-gcc-4.9.4<br>df5361f-IGB-gcc-4.9.4
+
|0.34-IGB-gcc-4.9.4-Python-3.6.1
−
|Analyze your assembly by comparing it to a reference genome
+
|PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes.
 
|-
 
|-
−
|[https://www.realtimegenomics.com/products/rtg-tools rtg-tools]
+
|[http://broadinstitute.github.io/picard/ picard]
−
|3.8.4
+
|2.10.1-Java-1.8.0_121<br>2.10.1-Java-1.8.0_152<br>2.9.0-Java-1.8.0_121<br>2.9.4-Java-1.8.0_121
−
|RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats.
+
|A set of tools (in Java) for working with next generation sequencing data in the BAM  (http://samtools.github.io/hts-specs) format.
 
|-
 
|-
−
|[https://github.com/biocore-ntnu/epic epic]
+
|[http://zlib.net/pigz/ pigz]
−
|0.2.9-IGB-gcc-4.9.4-Python-2.7.13
+
|2.3.4-IGB-gcc-4.9.4
−
|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.  
+
|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://valgrind.org/downloads/ valgrind]
+
|[https://github.com/broadinstitute/pilon pilon]
−
|3.13.0-IGB-gcc-4.9.4
+
|1.22-Java-1.8.0_121<br>1.23-Java-1.8.0_152
−
|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.
+
|Pilon is a software tool which can be used to:- Automatically improve draft assemblies- Find variation among strains, including large event detection
 
|-
 
|-
−
|[https://github.com/YeoLab/clipper clipper]
+
|[http://smithlabresearch.org/software/piranha/ piranha]
−
|1.2.1-IGB-gcc-4.9.4-Python-2.7.13
+
|1.2.1-IGB-gcc-4.9.4
−
|A tool to detect CLIP-seq peaks.
+
|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.  
 
|-
 
|-
−
|[http://github.com/wolever/nose-parameterized nose-parameterized]
+
|pixman
−
|0.6.0-IGB-gcc-4.9.4-Python-2.7.13
+
|
−
|Parameterized testing with any Python test framework.
+
|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://www.doxygen.org Doxygen]
+
|pkg-config
−
|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.
+
|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). - Homepage: http://www.freedesktop.org/wiki/Software/pkg-config/
 
|-
 
|-
−
|[http://csg.sph.umich.edu/liyanmin/vcfCodingSnps/index.shtml vcfCodingSnps]
+
|[https://github.com/soedinglab/plass plass]
−
|1.5
+
|2-c7e35-IGB-gcc-4.9.4<br>3-764a3
−
|vcfCodingSnps is a SNP annotation tool that annotates coding variants in VCF files.  
+
|Plass (Protein-Level ASSembler) is a software to assemble short read sequencing data on a protein level.  
 
|-
 
|-
−
|[http://blast.ncbi.nlm.nih.gov/ BLAST]
+
|[http://platanus.bio.titech.ac.jp/platanus-assembler platanus]
−
|2.2.26-Linux_x86_64
+
|1.2.4
−
|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.
+
|Platanus is a novel de novo sequence assembler that can reconstruct genomic sequences ofhighly heterozygous diploids from massively parallel shotgun sequencing data.
 
|-
 
|-
−
|[http://www.cse.lehigh.edu/~chen/software.htm VASP-E]
+
|[https://www.cog-genomics.org/plink2 plink]
−
|20190225-IGB-gcc-4.9.4<br>20191112-IGB-gcc-4.9.4
+
|1.07<br>1.90
−
|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.
+
|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.  
 
|-
 
|-
−
|[http://fulcrumgenomics.github.io/fgbio/ fgbio]
+
|[https://github.com/nanoporetech/pomoxis pomoxis]
−
|0.6.0-Java-1.8.0_152
+
|0.1.0-IGB-gcc-4.9.4-Python-3.6.1
−
|fgbio is a command line toolkit for working with genomic and particularly next generation sequencing data.
+
|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.
 
|-
 
|-
−
|[http://jupyter.org/ jupyter]
+
|poppler
−
|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.
+
|Poppler is a PDF rendering library based on the xpdf-3.0 code base.
 
|-
 
|-
−
|[http://rseqc.sourceforge.net/ RSeQC]
+
|[https://github.com/arq5x/poretools poretools]
−
|2.6.4-IGB-gcc-4.9.4-Python-2.7.13
+
|0.6.0-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.
+
|a toolkit for working with nanopore sequencing data from Oxford Nanopore. - Homepage: https://github.com/arq5x/poretools
 
|-
 
|-
−
|[http://trac.osgeo.org/geos geos]
+
|[http://matsen.fhcrc.org/pplacer/ pplacer]
−
|3.7.1-IGB-gcc-4.9.4
+
|1.1.alpha19
−
|GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite
+
|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://www.sanger.ac.uk/science/tools/ssaha2-0 ssaha2]
+
|[http://smithlabresearch.org/software/preseq/ preseq]
−
|2.5.5-IGB-gcc-4.9.4
+
|2.0.3-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.
+
|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://trinityrnaseq.github.io/ Trinity]
+
|[http://www.primer3.org primer3]
−
|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
+
|2.4.0-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.
+
|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://cran.r-project.org/web/packages/ncdf4 ncdf4]
+
|[http://prinseq.sourceforge.net/ prinseq]
−
|1.16-IGB-gcc-4.9.4-R-3.3.3
+
|0.20.4-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.
+
|PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data.  
 
|-
 
|-
−
|[https://ccb.jhu.edu/software/kraken/ Kraken2]
+
|[https://github.com/tseemann/prokka prokka]
−
|2.0.8-beta-IGB-gcc-4.9.4
+
|1.13-IGB-gcc-4.9.4-Perl-5.24.1<br>1.14.6-IGB-gcc-4.9.4-Perl-5.24.1
−
|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.  
+
|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://hannonlab.cshl.edu/fastx_toolkit/ FASTX-Toolkit]
+
|[https://github.com/google/protobuf protobuf]
−
|0.0.14-IGB-gcc-4.9.4
+
|2.6.1-IGB-gcc-4.9.4<br>3.5.0-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/
+
|Protocol Buffers (a.k.a., protobuf) are Googles language-neutral, platform-neutral, extensible mechanism for serializing structured data.
 
|-
 
|-
−
|[http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?signalp SignalP]
+
|[https://github.com/lilydjwg/pssh pssh]
−
|4.1
+
|2.3.1-IGB-gcc-4.9.4-Python-2.7.13
−
|Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
+
|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.
 
|-
 
|-
−
|[http://busco.ezlab.org/ BUSCO]
+
|[https://daler.github.io/pybedtools/main.html pybedtools]
−
|3.0.1-IGB-gcc-4.9.4-Python-2.7.13
+
|0.7.10-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|pybedtools is a Python package that wraps BEDTools, so you will need both installed.
 
|-
 
|-
−
|[https://forge-dga.jouy.inra.fr/projects/hapflk hapflk]
+
|[https://github.com/brentp/pyfasta/ pyfasta]
−
|1.4-IGB-gcc-4.9.4-Python-3.6.1
+
|0.5.2-IGB-gcc-4.9.4-Python-2.7.13
−
|hapflk is a software implementing the hapFLK and FLK tests for the detection of selection signatures based on multiple population genotyping data.
+
|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://github.com/PacificBiosciences/GenomicConsensus GenomicConsensus]
+
|[http://deeplearning.net/software/libgpuarray pygpu]
−
|3.0.2-IGB-gcc-4.9.4-Python-2.7.13
+
|0.6.5-IGB-gcc-4.9.4-Python-2.7.13
−
|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.
+
|Python bindings for libgpuarray - Homepage: http://deeplearning.net/software/libgpuarray
 
|-
 
|-
−
|cURL
+
|[https://pygraphviz.github.io/ pygraphviz]
−
|
+
|1.3.1-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|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://www.mothur.org/ Mothur]
+
|[https://github.com/lisa-lab/pylearn2 pylearn2]
−
|1.38.1.1<br>1.39.5<br>1.39.5-IGB-gcc-4.9.4
+
|20170525-IGB-gcc-4.9.4-Python-2.7.13
−
|Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
+
|Pylearn2 is a library designed to make machine learning research easy. - Homepage: https://github.com/lisa-lab/pylearn2
 
|-
 
|-
−
|[https://github.com/tensorflow/models TensorFlowModels]
+
|[http://qualimap.bioinfo.cipf.es/ qualimap]
−
|1.11-IGB-gcc-4.9.4-Python-3.6.1<br>20171113-IGB-gcc-4.9.4-Python-3.6.1
+
|2.2.1-Java-1.8.0_121
−
|This repository contains a number of different models implemented in TensorFlow:
+
|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.
 
|-
 
|-
−
|[http://www.hdfgroup.org/HDF5/ HDF5]
+
|[https://sourceforge.net/projects/quast/ quast]
−
|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
+
|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
−
|HDF5 is a unique technology suite that makes possible the management of extremely large and complex data collections.
+
|QUAST performs fast and convenient quality evaluation and comparison of genome assemblies.  
 
|-
 
|-
−
|x264
+
|[https://github.com/mahulchak/quickmerge quickmerge]
−
|
+
|0.2-IGB-gcc-4.9.4-Python-2.7.13
−
|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. - Homepage: http://www.videolan.org/developers/x264.html
+
|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.
 
|-
 
|-
−
|[https://github.com/TGAC/KAT KAT]
+
|[http://rnaseq-mats.sourceforge.net/ rMATS]
−
|2.4.1-IGB-gcc-4.9.4
+
|3.2.5-IGB-gcc-4.9.4-Python-2.7.13
−
|KAT is a suite of tools that analyse jellyfish hashes or sequence files (fasta or fastq) using kmer counts.
+
|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://www.sentieon.com/ sentieon]
 
−
|201808
 
−
|A fast and accurate solution to variant calling from next-generation sequence data
 
−
|-
 
−
|[http://www.ece.uvic.ca/~frodo/jasper/ JasPer]
 
−
|1.900.1-IGB-gcc-4.9.4<br>2.0.10-IGB-gcc-4.9.4
 
−
|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. - Homepage: http://www.ece.uvic.ca/~frodo/jasper/
 
−
|-
 
−
|[http://www.sanger.ac.uk/science/tools/ssaha2-0 ssaha_pileup]
 
−
|0.6-IGB-gcc-4.9.4
 
−
|SSAHA2: Sequence Search and Alignment by Hashing Algorithm
 
 
|-
 
|-
 
|[https://github.com/isovic/racon racon]
 
|[https://github.com/isovic/racon racon]
Line 2,161: Line 2,185:
 
|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.
 
|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.
 
|-
 
|-
−
|[http://openbabel.org OpenBabel]
+
|[http://catchenlab.life.illinois.edu/radinitio/ radinitio]
−
|3.0.0-IGB-gcc-8.2.0
+
|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
−
|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.
+
|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.
 
|-
 
|-
−
|[https://github.com/LynchLab/MAPGD MAPGD]
+
|[http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/ randfold]
−
|0.4.26-IGB-gcc-4.9.4
+
|2.0.1-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.
+
|Minimum free energy of folding randomization test software
 
|-
 
|-
−
|[http://genometools.org/ genometools]
+
|[https://rclone.org/ rclone]
−
|1.5.10-IGB-gcc-4.9.4
+
|1.41
−
|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.
+
|Rclone is a command line program to sync files and directories to and from different cloud storage
 
|-
 
|-
−
|[https://github.com/BinPro/CONCOCT CONCOCT]
+
|[https://github.com/biocore/redbiom redbiom]
−
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
+
|0.3.2-IGB-gcc-4.9.4-Python-3.6.1
−
|A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
+
|Redbiom is a cache service for sample metadata and sample data.  
 
|-
 
|-
−
|[http://http://sox.sourceforge.net/ SoX]
+
|[https://cran.r-project.org/web/packages/rgeos/index.html rgeos]
−
|14.4.2-IGB-gcc-4.9.4
+
|0.4-2-IGB-gcc-4.9.4-R-3.5.0
−
|Sound eXchange, the Swiss Army knife of audio manipulation
+
|nterface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries.
 
|-
 
|-
−
|lzo
+
|[https://github.com/Kingsford-Group/rnaseqtools rnaseqtools]
−
|
+
|1.0.2-IGB-gcc-4.9.4
−
|Portable lossless data compression library
+
|This repo rnaseqtools provides a set of tools to process transcripts (mainly in gtf format).
 
|-
 
|-
−
|ATK
+
|[https://root.cern.ch/ root]
−
|
+
|6.14.06-IGB-gcc-4.9.4
−
|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.
+
|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.
 
|-
 
|-
−
|[https://github.com/marbl/canu Canu]
+
|[https://www.rosettacommons.org/ rosetta]
−
|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
+
|2017.52-IGB-gcc-4.9.4
−
|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).
+
|The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.  
 
|-
 
|-
−
|[https://bitbucket.org/biobakery/metaphlan2 metaphlan2]
+
|[http://rpy.sourceforge.net/ rpy]
−
|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
+
|1.0.3-IGB-gcc-4.9.4-Python-2.7.13-R-2.15.3
−
|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.
+
|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://clusterflow.io/ clusterflow]
+
|[http://rpy.sourceforge.net/ rpy2]
−
|0.5-IGB-gcc-4.9.4-Perl-5.24.1
+
|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>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
−
|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.
+
|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/vgteam/vg vg]
+
|[https://www.realtimegenomics.com/products/rtg-tools rtg-tools]
−
|1.15.0
+
|3.8.4
−
|variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
+
|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://github.com/brianbeliveau/OligoMiner OligoMiner]
+
|[https://github.com/najoshi/sabre sabre]
−
|20181123-IGB-gcc-4.9.4
+
|20171114-IGB-gcc-4.9.4
−
|A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
+
|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.
 
|-
 
|-
−
|efiest/devel
+
|[http://lomereiter.github.io/sambamba/ sambamba]
−
|devel
+
|0.6.6
−
|
+
|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.
 
|-
 
|-
−
|[http://vfsmspineagent.fsm.northwestern.edu/ AGEnt]
+
|[https://github.com/GregoryFaust/samblaster samblaster]
−
|0.2.1-IGB-gcc-4.9.4
+
|0.1.24-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.
+
|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.
 
|-
 
|-
−
|[https://github.com/pgmpy/pgmpy pgmpy]
+
|[https://github.com/Kingsford-Group/scallop scallop]
−
|20180320-IGB-gcc-4.9.4-Python-3.6.1
+
|0.10.3-IGB-gcc-4.9.4<br>0.10.4-IGB-gcc-4.9.4
−
|pgmpy is a python library for working with Probabilistic Graphical Models.
+
|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://projects.coin-or.org/ADOL-C ADOL-C]
+
|[https://github.com/lebedov/scikit-cuda scikit-cuda]
−
|2.6.3-IGB-gcc-4.9.4
+
|0.5.1-IGB-gcc-4.9.4-Python-2.7.13
−
|ADOL-C is an open-source package for the automatic differentiation of C and C++ programs.  
+
|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.
 
|-
 
|-
−
|[http://genome.ucsc.edu/FAQ/FAQblat.html BLAT]
+
|[https://github.com/nanoporetech/scrappie scrappie]
−
|3.5-IGB-gcc-4.9.4
+
|1.3.0-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.
+
|Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group.
 
|-
 
|-
−
|[https://skylign.org/ skylign]
+
|[https://www.sentieon.com/ sentieon]
−
|1.1-IGB-gcc-4.9.4-Perl-5.24.1
+
|201808
−
|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.
+
|A fast and accurate solution to variant calling from next-generation sequence data
 
|-
 
|-
−
|[http://pb-falcon.readthedocs.io/en/latest/index.html FALCON]
+
|[https://www.seqan.de/ seqan]
−
|1.8.8-IGB-gcc-4.9.4-Python-2.7.13
+
|2.3.2-IGB-gcc-4.9.4
−
|FALCON is a diploid aware genome assembler designed for Pacific Biosciences long read data.
+
|SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data
 
|-
 
|-
−
|[http://www.genome.umd.edu/masurca.html MaSuRCA]
+
|[https://github.com/lh3/seqtk/ seqtk]
−
|3.2.3-IGB-gcc-4.9.4
+
|1.2-IGB-gcc-4.9.4<br>1.2-IGB-gcc-8.2.0<br>1.3-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).
+
|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.
 
|-
 
|-
−
|[http://search.cpan.org/~lds/GD/ GD]
+
|[https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html shapeit]
−
|2.66-IGB-gcc-4.9.4-Perl-5.24.1
+
|2.20
−
|GD.pm - Interface to Gd Graphics Library
+
|SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
 
|-
 
|-
−
|[https://www.tensorflow.org/ Tensorflow]
+
|[https://www.gnu.org/software/sharutils/ sharutils]
−
|1.2.1-IGB-gcc-4.9.4-Python-2.7.13
+
|4.15.2-IGB-gcc-4.9.4
−
|An open-source software library for Machine Intelligence
+
|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.
 
|-
 
|-
−
|[http://www.unidata.ucar.edu/software/netcdf/ netCDF-Fortran]
+
|[https://github.com/chanzuckerberg/shasta shasta]
−
|4.4.1-IGB-gcc-4.9.4
+
|0.2.0
−
|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.
+
|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.
 
|-
 
|-
−
|[https://github.com/lvclark/tagdigger tagdigger]
+
|shortbred/prod
−
|1.1-IGB-gcc-4.9.4-Python-3.6.1
+
|prod
−
|TagDigger is a program for processing FASTQ files from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) experiments.
+
|
 
|-
 
|-
−
|[https://sourceforge.net/projects/biogrinder/ Grinder]
+
|singularity
−
|0.5.4-IGB-gcc-4.9.4-Perl-5.24.1
+
|3.4.1
−
|Grinder is a versatile open-source bioinformatic tool to create simulated omic shotgun and amplicon sequence libraries for all main sequencing platforms.
+
|Application and environment virtualization
 
|-
 
|-
−
|[http://www.repeatmasker.org/RepeatModeler/ RepeatScout]
+
|[https://skylign.org/ skylign]
−
|1.0.5-IGB-gcc-4.9.4
+
|1.1-IGB-gcc-4.9.4-Perl-5.24.1
−
|De Novo Repeat Finder,
+
|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.
 
|-
 
|-
−
|[https://github.com/slowkoni/rfmix RFMix]
+
|[https://www.pacb.com/support/software-downloads/ smrtlink]
−
|20180503-IGB-gcc-4.9.4
+
|8.0.0.80529
−
|A discriminative method for local ancestry inference
+
|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://community.nanoporetech.com/posts/pre-release-of-stand-alone guppy]
+
|[http://lowelab.ucsc.edu/snoscan/ snoscan]
−
|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
+
|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
−
|Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.  
+
|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
 +
|SnpEff is a variant annotation and effect prediction tool.  It annotates and predicts the effects of genetic variants (such as amino acid changes).
 
|-
 
|-
−
|freetype
+
|[https://github.com/magnusmanske/snpomatic snpomatic]
−
|
+
|1.0-IGB-gcc-4.9.4
−
|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.
+
|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://github.com/biota/sourcetracker2 sourcetracker]
 
|[https://github.com/biota/sourcetracker2 sourcetracker]
Line 2,281: Line 2,309:
 
|Bayesian community-wide culture-independent microbial source tracking
 
|Bayesian community-wide culture-independent microbial source tracking
 
|-
 
|-
−
|[https://github.com/DReichLab/AdmixTools AdmixTools]
+
|[https://support.10xgenomics.com/spatial-gene-expression/software/pipelines/latest/what-is-space-ranger spaceranger]
−
|1.0.1-IGB-gcc-4.9.4
+
|1.0.0
−
|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.
+
|Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield 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.
 
|-
 
|-
−
|[http://python.org/ Python]
+
|[https://github.com/sparsehash/sparsehash sparsehash]
−
|2.7.13-IGB-gcc-4.9.4<br>3.6.1-IGB-gcc-4.9.4<br>3.7.2-IGB-gcc-8.2.0
+
|2.0.3-IGB-gcc-4.9.4
−
|Python is a programming language that lets you work more quickly and integrate your systems more effectively.
+
|This directory contains several hash-map implementations, similar inAPI to SGIs hash_map class, but with different performance characteristics.
 
|-
 
|-
−
|[https://github.com/voutcn/megahit MEGAHIT]
+
|[http://eddylab.org/software.html squid]
−
|1.1.1-IGB-gcc-4.9.4
+
|1.9g-IGB-gcc-4.9.4
−
|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. - Homepage: https://github.com/voutcn/megahit
+
|A C library that is bundled with much of the above software. C function library for sequence analysis.
 
|-
 
|-
−
|[https://github.com/nanoporetech/megalodon/ megalodon]
+
|[http://www.sanger.ac.uk/science/tools/ssaha2-0 ssaha2]
−
|1.0.0-IGB-gcc-4.9.4-Python-3.6.1
+
|2.5.5-IGB-gcc-4.9.4
−
|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.
+
|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.
 
|-
 
|-
−
|[https://www.rosettacommons.org/ rosetta]
+
|[http://www.sanger.ac.uk/science/tools/ssaha2-0 ssaha_pileup]
−
|2017.52-IGB-gcc-4.9.4
+
|0.6-IGB-gcc-4.9.4
−
|The Rosetta software suite includes algorithms for computational modeling and analysis of protein structures.
+
|SSAHA2: Sequence Search and Alignment by Hashing Algorithm
 
|-
 
|-
−
|[https://github.com/nf-core/tools nf-core]
+
|[http://www.crypticlineage.net/pages/software.html strauto]
−
|1.6-IGB-gcc-4.9.4-Python-3.6.1
+
|1-IGB-gcc-4.9.4
−
|A python package with helper tools for the nf-core community.
+
|Automation and Parallelization of STRUCTURE Analysis
 
|-
 
|-
−
|[http://www.swig.org/ SWIG]
+
|[https://github.com/Illumina/strelka strelka]
−
|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
+
|2.9.9
−
|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/
+
|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://hmmer.org/ HMMER]
+
|[https://github.com/gpertea/stringtie stringtie]
−
|2.3.2-IGB-gcc-4.9.4<br>3.1b2-IGB-gcc-4.9.4<br>3.2.1-IGB-gcc-4.9.4
+
|2.1.1-IGB-gcc-4.9.4
−
|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.
+
|Transcript assembly and quantification for RNA-Seq
 
|-
 
|-
−
|pkg-config
+
|[https://web.stanford.edu/group/pritchardlab/structure.html structure]
−
|
+
|2.3.4-IGB-gcc-4.9.4
−
|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). - Homepage: http://www.freedesktop.org/wiki/Software/pkg-config/
+
|The program structure is a free software package for using multi-locus genotype data to investigate population structure.
 
|-
 
|-
−
|[http://www.usadellab.org/cms/?page=trimmomatic Trimmomatic]
+
|[http://swift-lang.org/Swift-T/ swift-t]
−
|0.36-Java-1.8.0_121<br>0.36-Java-1.8.0_152<br>0.38-Java-1.8.0_152
+
|1.3-IGB-gcc-4.9.4
−
|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.  
+
|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.  
 
|-
 
|-
−
|poppler
+
|[https://www.synapse.org/ synapseclient]
−
|
+
|1.9.2-IGB-gcc-4.9.4-Python-3.6.1
−
|Poppler is a PDF rendering library based on the xpdf-3.0 code base.
+
|Synapse is an open source software platform that data scientists can use to carry out, track, and communicate their research in real time.
 
|-
 
|-
−
|[https://github.com/tseemann/barrnap barrnap]
+
|[https://t3f.readthedocs.io/en/latest/index.html t3f]
−
|0.9-IGB-gcc-4.9.4
+
|1.1.0-IGB-gcc-4.9.4-Python-3.6.1
−
|Barrnap predicts the location of ribosomal RNA genes in genomes.  
+
|t3f is a library for working with Tensor Train decomposition.  
 
|-
 
|-
−
|[https://www.rust-lang.org Rust]
+
|[http://lowelab.ucsc.edu/tRNAscan-SE/ tRNAscan-SE]
−
|1.41.1<br>1.41.1-IGB-gcc-8.2.0
+
|1.3.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded
−
|Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
+
|tRNAscan-SE: a tool for finding transfer RNAs
 
|-
 
|-
−
|[http://mafft.cbrc.jp/alignment/software/ MAFFT]
+
|[http://samtools.sourceforge.net tabix]
−
|7.310-IGB-gcc-4.9.4
+
|0.2.6-IGB-gcc-4.9.4
−
|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. - Homepage: http://mafft.cbrc.jp/alignment/software/
+
|Generic indexer for TAB-delimited genome position files
 
|-
 
|-
−
|PROJ
+
|[https://github.com/lvclark/tagdigger tagdigger]
−
|
+
|1.1-IGB-gcc-4.9.4-Python-3.6.1
−
|Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
+
|TagDigger is a program for processing FASTQ files from genotyping-by-sequencing (GBS) or restriction site-associated DNA sequencing (RAD-seq) experiments.
 
|-
 
|-
 
|[http://www.gnu.org/software/tar/tar.html tar]
 
|[http://www.gnu.org/software/tar/tar.html tar]
Line 2,345: Line 2,373:
 
|tar: The GNU tape archiver
 
|tar: The GNU tape archiver
 
|-
 
|-
−
|[https://www.rarlab.com/ unrar]
+
|tbb
−
|5.7.3-IGB-gcc-4.9.4
+
|
−
|RAR is a powerful archive manager.
+
|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.
 
|-
 
|-
−
|[ftp://ftp.ebi.ac.uk/pub/databases/Pfam/Tools/README pfamscan]
+
|[https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ tbl2asn]
−
|1.6-IGB-gcc-4.9.4-Perl-5.24.1
+
|20180516<br>20190117<br>20200203
−
|This readme should help you get started with "pfam_scan.pl", which is for usewith the HMMER3 version of HMMER.
+
|Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank
 
|-
 
|-
−
|[https://github.com/magnusmanske/snpomatic snpomatic]
+
|[https://github.com/lanpa/tensorboardX tensorboardX]
−
|1.0-IGB-gcc-4.9.4
+
|1.9-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|TensorBoardX lets you watch Tensors Flow without Tensorflow
 
|-
 
|-
−
|[http://www.biostat.jhsph.edu/~hji/cisgenome/ cisgenome]
+
|[http://tensorly.org/stable/home.html tensorly]
−
|2.0-IGB-gcc-4.9.4
+
|0.4.2-IGB-gcc-4.9.4-Python-3.6.1
−
|An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
+
|Simple and Fast Tensor Learning in Python
 
|-
 
|-
−
|[http://www.zeromq.org/ ZeroMQ]
+
|[https://github.com/nanoporetech/tombo/ tombo]
−
|4.2.2-IGB-gcc-4.9.4
+
|1.5-IGB-gcc-4.9.4-Python-3.6.1
−
|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.
+
|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://www.bioinformatics.babraham.ac.uk/projects/fastqc/ FastQC]
+
|[http://hibberdlab.com/transrate/ transrate]
−
|0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152<br>0.11.8-IGB-gcc-4.9.4-Java-1.8.0_152<br>0.11.8-Java-1.8.0_152
+
|1.0.3
−
|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.
+
|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.
 
|-
 
|-
−
|PCRE
+
|[https://github.com/laurikari/tre tre]
−
|
+
|20161208-IGB-gcc-4.9.4
−
|The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.
+
|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.
 
|-
 
|-
−
|[http://www.atgc-montpellier.fr/fastme/binaries.php FastME]
+
|[https://bitbucket.org/nygcresearch/treemix treemix]
−
|2.1.6.1-IGB-gcc-4.9.4
+
|1.13-IGB-gcc-4.9.4
−
|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.
+
|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.
 
|-
 
|-
−
|[https://github.com/seqan/flexbar flexbar]
+
|[http://tandem.bu.edu/trf/trf.html trf]
−
|3.0.3-IGB-gcc-4.9.4
+
|4.0.9
−
|The program Flexbar preprocesses high-throughput sequencing data efficiently. It demultiplexes barcoded runs and removes adapter sequences. Moreover, trimming and filtering features are provided.  
+
|Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.  
 
|-
 
|-
−
|[https://github.com/halelab/GBS-SNP-CROP GBS-SNP-CROP]
+
|[https://experts.illinois.edu/en/publications/truesight-self-training-algorithm-for-splice-junction-detection-u truesight]
−
|4.0-IGB-gcc-4.9.4
+
|0.06-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.
+
|A Self-training Algorithm for Splice Junction Detection using RNA-seq.
 
|-
 
|-
−
|[http://rpy.sourceforge.net/ rpy]
+
|udunits
−
|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.
+
|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://github.com/ekg/freebayes FreeBayes]
+
|[https://github.com/CGATOxford/UMI-tools umi-tools]
−
|1.1.0-IGB-gcc-4.9.4
+
|1.0.1-IGB-gcc-8.2.0-Python-3.7.2
−
|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.
+
|Tools for handling Unique Molecular Identifiers in NGS data sets
 
|-
 
|-
−
|[https://github.com/nanoporetech/tombo/ tombo]
+
|[https://github.com/PacificBiosciences/unanimity/ unanimity]
−
|1.5-IGB-gcc-4.9.4-Python-3.6.1
+
|20180307-IGB-gcc-4.9.4
−
|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.
+
|C++ library and its applications to generate and process accurate consensus sequences
 
|-
 
|-
−
|[http://zlib.net/pigz/ pigz]
+
|[https://www.rarlab.com/ unrar]
−
|2.3.4-IGB-gcc-4.9.4
+
|5.7.3-IGB-gcc-4.9.4
−
|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.  
+
|RAR is a powerful archive manager.
 
|-
 
|-
−
|[https://bitbucket.org/nsegata/lefse LEfSe]
+
|[https://www.kernel.org/pub/linux/utils/util-linux util-linux]
−
|20180219-IGB-gcc-4.9.4-Python-2.7.13
+
|2.34-IGB-gcc-4.9.4
−
|LEfSe
+
|Set of Linux utilities
 
|-
 
|-
−
|[https://github.com/neufeld/pandaseq PANDAseq]
+
|[http://valgrind.org/downloads/ valgrind]
−
|2.11-IGB-gcc-4.9.4
+
|3.13.0-IGB-gcc-4.9.4
−
|PANDAseq assembles Illumina Solexa overlapping pair-end reads. - Homepage: https://github.com/neufeld/pandaseq
+
|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.
 
|-
 
|-
−
|[https://github.com/HRGV/phyloFlash phyloFlash]
+
|[http://csg.sph.umich.edu/liyanmin/vcfCodingSnps/index.shtml vcfCodingSnps]
−
|3.3-IGB-gcc-4.9.4
+
|1.5
−
|phyloFlash is a pipeline to rapidly reconstruct the SSU rRNAs and explore phylogenetic composition of an Illumina (meta)genomic or transcriptomic dataset.
+
|vcfCodingSnps is a SNP annotation tool that annotates coding variants in VCF files.  
 
|-
 
|-
−
|[https://gdc.cancer.gov/access-data/gdc-data-transfer-tool gdc-client]
+
|[https://github.com/vcflib/vcflib vcflib]
−
|1.3.0-IGB-gcc-4.9.4-Python-2.7.13
+
|1.0.0-rc2-IGB-gcc-8.2.0
−
|The GDC Data Transfer Tool Client provides a command-line interface supporting both GDC data downloads and submissions.
+
|a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
 
|-
 
|-
−
|Phantompeaktools-spp
+
|[https://github.com/velocyto-team/velocyto.py velocyto]
−
|
+
|0.17.17-IGB-gcc-4.9.4-Python-3.6.1
−
|Custom SPP for Phantompeaktools
+
|Velocyto is a library for the analysis of RNA velocity.
 
|-
 
|-
−
|[http://bioinformatics.psb.ugent.be/supplementary_data/erbon/nov2003/ randfold]
+
|[https://github.com/velocyto-team/velocyto.R velocyto.R]
−
|2.0.1-IGB-gcc-4.9.4
+
|20190527-IGB-gcc-4.9.4-R-3.4.2
−
|Minimum free energy of folding randomization test software
+
|RNA velocity estimation in R
 
|-
 
|-
−
|[http://www.open-mpi.org/ OpenMPI]
+
|[https://www.ebi.ac.uk/~zerbino/velvet/ velvet]
−
|2.1.0-GCC-4.9.4-2.28<br>4.0.0-GCC-8.2.0-2.32
+
|1.2.10-IGB-gcc-4.9.4-kmer_121
−
|The Open MPI Project is an open source MPI-3 implementation.
+
|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://www.gnu.org/software/sharutils/ sharutils]
+
|[https://github.com/vgteam/vg vg]
−
|4.15.2-IGB-gcc-4.9.4
+
|1.15.0
−
|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.
+
|variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
 
|-
 
|-
−
|[http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html gtool]
+
|[https://github.com/ruanjue/wtdbg2 wtdbg2]
−
|0.7.5
+
|2.3-IGB-gcc-4.9.4
−
|GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.  
+
|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.
 
|-
 
|-
−
|[http://homer.ucsd.edu/homer/ HOMER]
+
|x264
−
|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.
+
|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. - Homepage: http://www.videolan.org/developers/x264.html
 
|-
 
|-
−
|[https://lftp.yar.ru/ lftp]
+
|[https://github.com/dmlc/xgboost xgboost]
−
|4.8.3
+
|0.80-IGB-gcc-4.9.4-Python-3.6.1
−
|FTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).  
+
|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.
 
|-
 
|-
−
|[https://www.ebi.ac.uk/~zerbino/velvet/ velvet]
+
|xorg-macros
−
|1.2.10-IGB-gcc-4.9.4-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.  
+
|X.org macros utilities.
 
|-
 
|-
−
|[http://microbiomeutil.sourceforge.net/ microbiomeutil]
+
|zlib
−
|20110519-IGB-gcc-4.9.4
+
|
−
|Contains ChimeraSlayer, WigeoN, and NAST-iEr
+
|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://bioinf.uni-greifswald.de/augustus/ augustus]
 
−
|3.2.3-IGB-gcc-4.9.4<br>3.3.2-IGB-gcc-4.9.4
 
−
|AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
 
−
|-
 
−
|[http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?tmhmm TMHMM]
 
−
|2.0c-IGB-gcc-4.9.4
 
−
|Transmembrane helices in proteins
 
−
|-
 
−
|[https://www.gams.com/ GAMS]
 
−
|23.6.5
 
−
|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/velocyto-team/velocyto.py velocyto]
 
−
|0.17.17-IGB-gcc-4.9.4-Python-3.6.1
 
−
|Velocyto is a library for the analysis of RNA velocity.
 
−
|-
 
−
|[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.
 
−
|-
 
−
|[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://cytoscape.org/ cytoscape]
 
−
|3.3.0-Java-1.8.0_152-2.8tb<br>3.3.0-Java-1.8.0_152-350gb<br>3.7.0-Java-1.8.0_152-2.8tb<br>3.7.0-Java-1.8.0_152-350gb
 
−
|Cytoscape is an open source software platform for visualizing complex networks and integrating these with any type of attribute data.
 
 
|}
 
|}

Revision as of 14:54, 2 April 2020

Application Installed Versions Description
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
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.
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.
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.
AMPHORA2 20190104-IGB-gcc-4.9.4 An Automated Phylogenomic Inference Pipeline for Bacterial and Archaeal Sequences.
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.
ARCS 1.0.0-IGB-gcc-4.9.4-Perl-5.24.1 Scaffolding genome sequence assemblies using 10X Genomics GemCode/Chromium data. - Homepage: https://github.com/bcgsc/arcs
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
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.
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.
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
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.
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
Assemblytics 3f570cd-IGB-gcc-4.9.4
df5361f-IGB-gcc-4.9.4 		Analyze your assembly by comparing it to a reference genome
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
BBMap 38.36-Java-1.8.0_152 BBTools is a suite of fast, multithreaded bioinformatics tools designed for analysis of DNA and RNA sequence data.
BCFtools 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
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.
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+ 2.6.0-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.
BRAKER 2.1.2-IGB-gcc-4.9.4 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.
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 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.
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 		Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
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 		BamTools provides both a programmers API and an end-users toolkit for handling BAM files.
BiG-SCAPE 20181115-IGB-gcc-4.9.4-Python-3.6.1 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)
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 		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-8.2.0-Python-3.7.2 		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.
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 		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.
Boost 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 		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 		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.
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/
CD-HIT 4.6.6-IGB-gcc-4.9.4 CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. - Homepage: http://weizhong-lab.ucsd.edu/cd-hit/
CMake CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.
CNVnator 0.3.3-IGB-gcc-4.9.4 a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads
CONCOCT 1.0.0-IGB-gcc-4.9.4-Python-3.6.1 A program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.
CUDA 10.0.130
8.0.61
8.0.61-IGB-gcc-4.9.4
9.0.176-IGB-gcc-4.9.4
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.
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.
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 		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).
CheckM 1.0.7-IGB-gcc-4.9.4-Python-2.7.13 CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes.
Circlator 1.5.1-IGB-gcc-4.9.4-Python-3.6.1 A tool to circularize genome assemblies.
Circos 0.69-4-IGB-gcc-4.9.4-Perl-5.24.1 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. - Homepage: http://www.circos.ca/
Clp Clp (Coin-or linear programming) is an open-source linear programming solver written in C++.
Clustal-Omega 1.2.4-IGB-gcc-4.9.4 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 - Homepage: http://www.clustal.org/omega/
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/
ConsensusCore 1.0.1-IGB-gcc-4.9.4-Python-2.7.13 ConsensusCore is a library of C++ algorithms for PacBio multiple sequence consensus that powers Quiver (Python) and ConsensusTools (.NET).
Cufflinks 2.2.1
2.2.1-IGB-gcc-4.9.4-b4fa050 		Transcript assembly, differential expression, and differential regulation for RNA-Seq
Cython 0.27.3-IGB-gcc-4.9.4-Python-2.7.13 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.
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
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.
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
0.9.9-IGB-gcc-4.9.4 		Accelerated BLAST compatible local sequence aligner
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.
DIYABC 2.1.0 a user-friendly approach to Approximate Bayesian Computation for inference on population history using molecular markers
DendroPy 4.4.0-IGB-gcc-4.9.4-Python-3.6.1 DendroPy is a Python library for phylogenetic computing.
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.
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.
EasyBuild 3.5.3
3.6.0
3.6.2
3.9.3 		EasyBuild is a software build and installation frameworkwritten in Python that allows you to install software in a structured,repeatable and robust way.
Eigen Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
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.
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).
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/
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).
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.
FFmpeg 3.3-IGB-gcc-4.9.4 A complete, cross-platform solution to record, convert and stream audio and video. - Homepage: https://www.ffmpeg.org/
FLAC 1.3.1-IGB-gcc-4.9.4 Programs and libraries for working with Free Lossless Audio Codec (FLAC) files.
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.
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.
FastME 2.1.6.1-IGB-gcc-4.9.4 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.
FastQC 0.11.5-IGB-gcc-4.9.4-Java-1.8.0_152
0.11.8-IGB-gcc-4.9.4-Java-1.8.0_152
0.11.8-Java-1.8.0_152 		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.
FastTree 2.1.10-IGB-gcc-4.9.4 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.
Flye 2.4.2-IGB-gcc-4.9.4-Python-2.7.13
2.7-IGB-gcc-4.9.4-Python-3.6.1 		Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies.
FreeBayes 1.1.0-IGB-gcc-4.9.4 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.
GAMS 23.6.5 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.
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 		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.
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.
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,...).
GD 2.66-IGB-gcc-4.9.4-Perl-5.24.1 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.
GEOS GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS)
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.
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.
GLib 2.62.3-IGB-gcc-4.9.4 GLib is one of the base libraries of the GTK+ project
GMAP 2018-05-30-IGB-gcc-4.9.4 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.
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.
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.
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 		The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications.
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/
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.
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 		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
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.
GenomicConsensus 3.0.2-IGB-gcc-4.9.4-Python-2.7.13 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.
GhostScript 9.21-IGB-gcc-4.9.4 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. - Homepage: http://ghostscript.com
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.
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.
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.
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.
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.
HISAT2 2.0.5-IGB-gcc-4.9.4
2.1.0-IGB-gcc-4.9.4 		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).
HMMER 2.3.2-IGB-gcc-4.9.4
3.1b2-IGB-gcc-4.9.4
3.2.1-IGB-gcc-4.9.4 		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.
HTSeq 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 1.4-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
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).
HarfBuzz HarfBuzz is an OpenType text shaping engine. - Homepage: http://www.freedesktop.org/wiki/Software/HarfBuzz
HiC-Pro 2.9.0-IGB-gcc-4.9.4-Python-2.7.13 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.
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.
IM-TORNADO 2.0.3.3-IGB-gcc-4.9.4-Python-2.7.13 A pipeline for 16S reads from paired-end libraries
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.
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
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
ImageMagick 7.0.5-5-IGB-gcc-4.9.4 ImageMagick is a software suite to create, edit, compose, or convert bitmap images - Homepage: http://www.imagemagick.org/
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 		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.
JUnit A programmer-oriented testing framework for Java.
Jalview 2.11.0-Java-1.8.0_152
JasPer 1.900.1-IGB-gcc-4.9.4
2.0.10-IGB-gcc-4.9.4 		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. - Homepage: http://www.ece.uvic.ca/~frodo/jasper/
Java 1.8.0_121
1.8.0_152
1.8.0_201
11.0.5 		Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.
Jellyfish 1.1.12-IGB-gcc-4.9.4
2.2.10-IGB-gcc-8.2.0
2.2.6-IGB-gcc-4.9.4 		Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
Juicer 1.13.02-Java-1.8.0_152 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.
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.
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
2.2.0-IGB-gcc-4.9.4-Python-3.6.1
2.2.4-IGB-gcc-4.9.4-Python-3.6.1 		Keras is a high-level neural networks API, written in Python and capable of running on top of TensorFlow, CNTK, or Theano.
KneadData 0.6.1-IGB-gcc-4.9.4-Python-3.6.1 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 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 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.
Krona 2.7-IGB-gcc-4.9.4-Perl-5.24.1 Interactively explore metagenomes and more from a web browser.
LAME 3.99.5-IGB-gcc-4.9.4 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
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/
LEfSe 20180219-IGB-gcc-4.9.4-Python-2.7.13 LEfSe
LINKS 1.8.5-IGB-gcc-4.9.4-Perl-5.24.1 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).
LLVM 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.
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
LibTIFF tiff: Library and tools for reading and writing TIFF data files
LibUUID 1.0.3-IGB-gcc-4.9.4 Portable uuid C library
LittleCMS 2.8-IGB-gcc-4.9.4 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/
Lua 5.1.5-IGB-gcc-4.9.4
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.
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 		Model Based Analysis for ChIP-Seq data
MAFFT 7.310-IGB-gcc-4.9.4 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. - Homepage: http://mafft.cbrc.jp/alignment/software/
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
3.01.1-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.
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.
MATLAB 2017a
2017b 		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 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.
MCL 14.137-IGB-gcc-4.9.4 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. - Homepage: http://micans.org/mcl/
MEGAHIT 1.1.1-IGB-gcc-4.9.4 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. - Homepage: https://github.com/voutcn/megahit
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 		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.
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.
MMseqs2 10-6d92c MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets.
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).
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.
MUMmer 3.23-IGB-gcc-4.9.4
4.0.0beta2-IGB-gcc-4.9.4 		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/
MaSuRCA 3.2.3-IGB-gcc-4.9.4 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).
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
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
5.5.58-IGB-gcc-4.9.4 		MariaDB An enhanced, drop-in replacement for MySQL.
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.
MaxQuant 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.
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.
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 MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
MetaGeneAnnotator 20080819-x86-64 MetaGeneAnnotator is a gene-finding program for prokaryote and phage.
MetaVelvet 1.2.02-IGB-gcc-4.9.4 An extension of Velvet assembler to de novo metagenome assembly from short sequence 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 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.
Mono An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
Mothur 1.38.1.1
1.39.5
1.39.5-IGB-gcc-4.9.4 		Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
MultiQC 0.9-IGB-gcc-4.9.4-Python-2.7.13
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 		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.
NASM 2.12.02-IGB-gcc-4.9.4 NASM: General-purpose x86 assembler
NCO 4.7.2-IGB-gcc-4.9.4 manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5
NGS 1.3.0-IGB-gcc-4.9.4 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. - Homepage: https://github.com/ncbi/ngs
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.
NanoPlot 1.18.2-IGB-gcc-4.9.4-Python-3.6.1 Plotting tool for long read sequencing data and alignments.
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.
Ninja 1.9.0-IGB-gcc-4.9.4 Ninja is a small build system with a focus on speed.
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.
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.
OligoMiner 20181123-IGB-gcc-4.9.4 A rapid, flexible environment for the design of genome-scale oligonucleotide in situ hybridization probes
OpenBLAS 0.2.19-GCC-4.9.4-2.28-LAPACK-3.7.0-test OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
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.
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 		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.
OrthoFinder 2.2.7
2.3.7-IGB-gcc-4.9.4 		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/
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.
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
PCRE 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.
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.
PITA 6-IGB-gcc-4.9.4 The PITA executable allows you to identify and score microRNA targets on UTRs.
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.
PROJ Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
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. - Homepage: http://www.pango.org/
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
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 Practical Extraction and Report Language
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
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.
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.
Platypus 20180622-IGB-gcc-4.9.4-Python-2.7.13 The Platypus variant caller.
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.
Prodigal 2.6.3 Fast, reliable protein-coding gene prediction for prokaryotic genomes.
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).
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/
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 		Tensors and Dynamic neural networks in Pythonwith strong GPU acceleration.
PyZMQ 16.0.2-IGB-gcc-4.9.4-Python-3.6.1 Python bindings for ZeroMQ
Pysam 0.13.0-IGB-gcc-4.9.4-Python-2.7.13
0.13.0-IGB-gcc-4.9.4-Python-3.6.1 		Pysam is a python module for reading and manipulating Samfiles. Its a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
Python 2.7.13-IGB-gcc-4.9.4
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.
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 		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 Qt is a comprehensive cross-platform C++ application framework.
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 		R is a free software environment for statistical computing and graphics.
RAxML 8.2.12-IGB-gcc-4.9.4 RAxML search algorithm for maximum likelihood based inference of phylogenetic trees.
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.
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
RFMix 20180503-IGB-gcc-4.9.4 A discriminative method for local ancestry inference
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.
RMBlast 2.6.0-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.
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 Ribosomal RNA sub units
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.
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)
RSAT 2018-08-04-IGB-gcc-4.9.4 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 		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.
Ragout 2.0-IGB-gcc-4.9.4 Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references.
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.
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 		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 1.0.11
RepeatScout 1.0.5-IGB-gcc-4.9.4 De Novo Repeat Finder,
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.
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
1.41.1-IGB-gcc-8.2.0 		Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
SAMtools 0.1.20-IGB-gcc-4.9.4
1.10-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.
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.
SDL2 2.0.4-IGB-gcc-4.9.4 SDL: Simple DirectMedia Layer, a cross-platform multimedia library
SEPP 20180223-IGB-gcc-4.9.4-Python-2.7.13 SEPP stands for "SATe-enabled Phylogenetic Placement", and addresses the problem of phylogenetic placement of short reads into reference alignments and trees.
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.
SNAP 2013-11-29-IGB-gcc-4.9.4 (Semi-HMM-based Nucleic Acid Parser) gene prediction tool
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.
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 		SPAdes . St. Petersburg genome assembler . is intended for both standard isolates and single-cell MDA bacteria assemblies.
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
SRA-Toolkit 2.8.2-1 The NCBI SRA Toolkit enables reading (dumping) of sequencing files from the SRA database and writing (loading) files into the .sra format - Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=std
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
2.7.3a-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.
SUNDIALS 2.6.2-IGB-gcc-4.9.4 SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers
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/
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 		Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data.
SalmonTools 20190604-IGB-gcc-8.2.0 Useful tools for working with Salmon output
ScaLAPACK The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
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.
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.
SignalP 4.1 Signal peptide and cleavage sites in gram+, gram- and eukaryotic amino acid sequences
SoX 14.4.2-IGB-gcc-4.9.4 Sound eXchange, the Swiss Army knife of audio manipulation
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.
Stacks 1.47-IGB-gcc-4.9.4 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.
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.
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 		High performance read alignment, quantification and mutation discovery
SuiteSparse 5.4.0-IGB-gcc-4.9.4-METIS-5.1.0 SuiteSparse is a collection of libraries manipulate sparse matrices.
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.
Szip Szip compression software, providing lossless compression of scientific data
TASSEL 5.2.28-Java-1.8.0_121 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
TMHMM 2.0c-IGB-gcc-4.9.4 Transmembrane helices in proteins
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.
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.
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:
Tensorflow 1.2.1-IGB-gcc-4.9.4-Python-2.7.13 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 		An open-source software library for Machine Intelligence
Theano 0.9.0-IGB-gcc-4.9.4-Python-2.7.13 Theano is a Python library that allows you to define, optimize,and evaluate mathematical expressions involving multi-dimensional arrays efficiently. - Homepage: http://deeplearning.net/software/theano
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.
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.
TransDecoder 5.1.0-IGB-gcc-4.9.4-Perl-5.24.1 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.
Trim_Galore 0.4.4-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.
Trimmomatic 0.36-Java-1.8.0_121
0.36-Java-1.8.0_152
0.38-Java-1.8.0_152 		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.
Trinity 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 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.
USEARCH 11.0.667
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.
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.
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.
VCFtools 0.1.15-IGB-gcc-4.9.4-Perl-5.24.1 The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. - Homepage: https://vcftools.github.io
VEP 92.4-IGB-gcc-4.9.4-Perl-5.24.1 VEP (Variant Effect Predictor) predicts the functional effects of genomic variants.
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
dev 		VICSIN = Viral, Integrative, and Conjugative Sequence Identification and Networking
VMD 1.9.3-IGB-gcc-4.9.4 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
VarScan 2.3.9-Java-1.8.0_152
ViennaRNA 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.
XZ 5.2.3-IGB-gcc-4.9.4
5.2.3-IGB-gcc-8.2.0 		xz: XZ utilities
Yasm Yasm: Complete rewrite of the NASM assembler with BSD license
ZeroMQ 4.2.2-IGB-gcc-4.9.4 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.
a2ps 4.14-IGB-gcc-4.9.4 a2ps-4.14: Formats an ascii file for printing on a postscript printer
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.
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
ant 1.10.1-Java-1.8.0_121
1.10.1-Java-1.8.0_152 		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 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.
anvio 5.5-IGB-gcc-4.9.4-Python-3.6.1
6.1-IGB-gcc-4.9.4-Python-3.6.1 		Anvi’o is an open-source, community-driven analysis and visualization platform for ‘omics data.
argtable Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. - Homepage: http://argtable.sourceforge.net/
aspera 3.7.6 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.
atactk 0.1.6-IGB-gcc-4.9.4-Python-2.7.13 a toolkit for ATAC-seq data
augustus 3.2.3-IGB-gcc-4.9.4
3.3.2-IGB-gcc-4.9.4 		AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
awscli 1.16.113-IGB-gcc-4.9.4-Python-3.6.1 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-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.
barrnap 0.9-IGB-gcc-4.9.4 Barrnap predicts the location of ribosomal RNA genes in genomes.
bax2bam 20171114-IGB-gcc-4.9.4 bax2bam converts the legacy PacBio basecall format (bax.h5) into the BAMbasecall format.
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.
bcl 4.0.0
beagle 03Jul18.40b-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.
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.
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
binutils binutils: GNU binary utilities
bio-rocker 1.2.0-IGB-gcc-4.9.4-Ruby-2.4.2 Accurately detecting functional genes in metagenomes.
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 		The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables.
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
breseq 0.31.0-IGB-gcc-4.9.4 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.
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.
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.
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
cdbfasta 20170316-IGB-gcc-4.9.4 CDB (Constant DataBase) indexing and retrieval tools for FASTA files
cellranger 2.1.0
2.1.1
3.0.0
3.0.1
3.1.0 		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-atac 1.1.0 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.
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.
cisgenome 2.0-IGB-gcc-4.9.4 An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis
clipper 1.2.1-IGB-gcc-4.9.4-Python-2.7.13 A tool to detect CLIP-seq peaks.
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.
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.
coreutils 8.28-IGB-gcc-4.9.4 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
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.
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
cuDNN 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-IGB-gcc-4.9.4-CUDA-9.0.176
7.1.4-IGB-gcc-4.9.4-CUDA-9.0.176
7.6.1.34-CUDA-10.0.130 		The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.
cutadapt 1.14-IGB-gcc-4.9.4-Python-2.7.13
1.17-IGB-gcc-4.9.4-Python-3.6.1 		Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cytoscape 3.3.0-Java-1.8.0_152-2.8tb
3.3.0-Java-1.8.0_152-350gb
3.7.0-Java-1.8.0_152-2.8tb
3.7.0-Java-1.8.0_152-350gb 		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.
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 		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.
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
distruct 2.2-IGB-gcc-4.9.4 Modified version of the original distruct.py
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.
efiest/beta beta
efiest/beta_private beta_private
efiest/devel devel
efiest/devlocal devlocal
efiest/efitools efitools/devlocal
efiest/prod prod
efiest/prod_private prod_private
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).
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.
exonerate 2.2.0-IGB-gcc-4.9.4 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.
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)
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 		A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
fastPHASE 20160330 astPHASE is a program to estimate missing genotypes and unobserved haplotypes.
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 		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 1.6.1-IGB-gcc-4.9.4 FDUPES is a program for identifying duplicate files residingwithin specified directories.
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.
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.
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.
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.
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.
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.
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.
gengetopt Gengetopt is a tool to write command line option parsing code for C programs. - Homepage: https://www.gnu.org/software/gengetopt/gengetopt.html
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.
geos 3.7.1-IGB-gcc-4.9.4 GEOS (Geometry Engine - Open Source) is a C++ port of the JTS Topology Suite
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.
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
git 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.
glproto X protocol and ancillary headers
gnuplot 4.6.7-IGB-gcc-4.9.4
5.0.6-IGB-gcc-4.9.4 		Portable interactive, function plotting utility - Homepage: http://gnuplot.sourceforge.net/
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 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.
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.
gtest 1.8.0-IGB-gcc-4.9.4 Googles C++ test framework
gtool 0.7.5 GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
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
3.4.5 		Guppy is a stand-alone data bioinformatic toolkit that provides Oxford Nanopore Technologies basecalling algorithm, along with a number of post-processing tools.
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 The h5py package provides both a high- and low-level interface to the HDF5 library from Python.
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.
help2man help2man produces simple manual pages from the --help and --version output of other commands.
hhsuite 3.2.0 The HH-suite is an open-source software package for sensitive protein sequence searching based on the pairwise alignment of hidden Markov models
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.
icorn 0.97-IGB-gcc-4.9.4 Inputs: Reference Sequence (FASTA) & reads (FASTQ) & information of short reads
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.
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.
ior 3.0.1-IGB-gcc-4.9.4 Parallel filesystem I/O benchmark
jansson 2.6-IGB-gcc-4.9.4 Jansson is a C library for encoding, decoding and manipulating JSON data.
jemalloc 5.0.1-IGB-gcc-4.9.4 jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
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 0.34.10-IGB-gcc-4.9.4-Python-3.6.1
0.35.6-IGB-gcc-4.9.4-Python-3.6.1
1.0.4-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.
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.
kentUtils 353-IGB-gcc-4.9.4 UCSC genome browser kent bioinformatic utilities
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.
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:
lbzip2 2.5-IGB-gcc-4.9.4 lbzip2 is a free, multi-threaded compression utility with support for bzip2 compressed file format.
lftp 4.8.3 FTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
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.
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. - Homepage: http://libgd.bitbucket.org/
libgdiplus An Open Source implementation of the GDI+ API
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 2.3.0-IGB-gcc-4.9.4 libHaru is a free, cross platform, open source library for generating PDF files. - Homepage: http://libharu.org/
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.
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
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).
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
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 Mixed Integer Linear Programming (MILP) solver
lumpy 0.3.0-IGB-gcc-4.9.4 A probabilistic framework for structural variant discovery.
lzo Portable lossless data compression library
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
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.
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.
megalodon 1.0.0-IGB-gcc-4.9.4-Python-3.6.1 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.
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.
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 1.5.1-IGB-gcc-4.9.4 photogrammetricprocessing of digital images and 3D spatial data generation
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.
microbiomeutil 20110519-IGB-gcc-4.9.4 Contains ChimeraSlayer, WigeoN, and NAST-iEr
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.
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
2.3-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
mirdeep 2.0.0.8-IGB-gcc-4.9.4 miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
nanopack 1.0.0-IGB-gcc-4.9.4-Python-3.6.1 Easily install all my long read processing and analysis scripts simultaneously.
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
0.6.0-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.
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-vdb 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. - Homepage: https://github.com/ncbi/ncbi-vdb
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.
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.
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 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.
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 		Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages.
nf-core 1.6-IGB-gcc-4.9.4-Python-3.6.1 A python package with helper tools for the nf-core community.
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.
nodejs 10.16.2-IGB-gcc-4.9.4
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.
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.
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 		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 1.14.1-IGB-gcc-4.9.4-Python-3.6.1 NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases.
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.
pairtools 0.3.0-IGB-gcc-4.9.4-Python-3.6.1 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.
pandoc 2.2.3.2 If you need to convert files from one markup format into another, pandoc is your swiss-army knife
parallel 20170622-IGB-gcc-4.9.4 parallel: GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
pb-assembly 0.0.6 PacBio Assembly Tool Suite
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 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.
pbzip2 1.1.13-IGB-gcc-4.9.4 PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines.
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).
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.
pgmpy 20180320-IGB-gcc-4.9.4-Python-3.6.1 pgmpy is a python library for working with Probabilistic Graphical Models.
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.
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.
picard 2.10.1-Java-1.8.0_121
2.10.1-Java-1.8.0_152
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.
pigz 2.3.4-IGB-gcc-4.9.4 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.
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.
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). - Homepage: http://www.freedesktop.org/wiki/Software/pkg-config/
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.
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.
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.
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.
poppler Poppler is a PDF rendering library based on the xpdf-3.0 code base.
poretools 0.6.0-IGB-gcc-4.9.4-Python-2.7.13 a toolkit for working with nanopore sequencing data from Oxford Nanopore. - Homepage: https://github.com/arq5x/poretools
pplacer 1.1.alpha19 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.
preseq 2.0.3-IGB-gcc-4.9.4 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.
prokka 1.13-IGB-gcc-4.9.4-Perl-5.24.1
1.14.6-IGB-gcc-4.9.4-Perl-5.24.1 		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.
protobuf 2.6.1-IGB-gcc-4.9.4
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.
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.
pybedtools 0.7.10-IGB-gcc-4.9.4-Python-3.6.1 pybedtools is a Python package that wraps BEDTools, so you will need both installed.
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.
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
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 		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.
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.
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 		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.
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.
randfold 2.0.1-IGB-gcc-4.9.4 Minimum free energy of folding randomization test software
rclone 1.41 Rclone is a command line program to sync files and directories to and from different cloud storage
redbiom 0.3.2-IGB-gcc-4.9.4-Python-3.6.1 Redbiom is a cache service for sample metadata and sample data.
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.
rnaseqtools 1.0.2-IGB-gcc-4.9.4 This repo rnaseqtools provides a set of tools to process transcripts (mainly in gtf format).
root 6.14.06-IGB-gcc-4.9.4 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.
rosetta 2017.52-IGB-gcc-4.9.4 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
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 		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.
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.
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.
sambamba 0.6.6 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.
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.
scrappie 1.3.0-IGB-gcc-4.9.4 Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group.
sentieon 201808 A fast and accurate solution to variant calling from next-generation sequence data
seqan 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
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.
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/prod prod
singularity 3.4.1 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.
smrtlink 8.0.0.80529 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.
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 		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.
sourcetracker 2.0.1-IGB-gcc-4.9.4-Python-3.6.1 Bayesian community-wide culture-independent microbial source tracking
spaceranger 1.0.0 Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield 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.
sparsehash 2.0.3-IGB-gcc-4.9.4 This directory contains several hash-map implementations, similar inAPI to SGIs hash_map class, but with different performance characteristics.
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.
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
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 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.
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.
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.
t3f 1.1.0-IGB-gcc-4.9.4-Python-3.6.1 t3f is a library for working with Tensor Train decomposition.
tRNAscan-SE 1.3.1-IGB-gcc-4.9.4-Perl-5.26.1-unthreaded tRNAscan-SE: a tool for finding transfer RNAs
tabix 0.2.6-IGB-gcc-4.9.4 Generic indexer for TAB-delimited genome position 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.
tar 1.32-IGB-gcc-8.2.0 tar: The GNU tape archiver
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 		Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank
tensorboardX 1.9-IGB-gcc-4.9.4-Python-3.6.1 TensorBoardX lets you watch Tensors Flow without Tensorflow
tensorly 0.4.2-IGB-gcc-4.9.4-Python-3.6.1 Simple and Fast Tensor Learning in Python
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.
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.
truesight 0.06-IGB-gcc-4.9.4 A Self-training Algorithm for Splice Junction Detection using RNA-seq.
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.
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
unrar 5.7.3-IGB-gcc-4.9.4 RAR is a powerful archive manager.
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.
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 a simple C++ library for parsing and manipulating VCF files, + many command-line utilities
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 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.
vg 1.15.0 variation graph data structures, interchange formats, alignment, genotyping, and variant calling methods
wtdbg2 2.3-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.
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. - Homepage: http://www.videolan.org/developers/x264.html
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.
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.
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