Difference between revisions of "Biocluster Applications"

Revision as of 02:26, 28 May 2014

Application	Installed Versions	Description
454	2.6, 2.7, 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.
AbundantOTU+	0.91b	AbundantOTU+ is the successor of AbundantOTU with additional functionality. AbundantOTU+ deals with sequences from rare species as well, compared to AbundantOTU!!
abyss	1.2.5, 1.3.3, 1.3.4	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.
afni	2011_12_21_2014	AFNI (which might be an acronym for Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. It runs on Unix+X11+Motif systems, including SGI, Solaris, Linux, and Mac OS X. It is available free (in C source code format, and some precompiled binaries) for research purposes.
allpathslg	42911	ALLPATHS-LG is our original short read assembler and it works on both small and large (mammalian size) genomes. To use it, you should first generate ~100 base Illumina reads from two libraries: one from ~180 bp fragments, and one from ~3000 bp fragments, both at about 45x coverage. Sequence from longer fragments will enable longer-range continuity.
amos	3.1.0	The AMOS consortium is committed to the development of open-source whole genome assembly software. The project acronym (AMOS) represents our primary goal -- to produce A Modular, Open-Source whole genome assembler.
AmpliconNoise	1.2.7	AmpliconNoise is a collection of programs for the removal of noise from 454 sequenced PCR amplicons. It involves two steps the removal of noise from the sequencing itself and the removal of PCR point errors. This project also includes the Perseus algorithm for chimera removal.
art	20110922	ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles.
augustus	2.6.1	AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
b2g4pipe	2.5	adds environmental variables to blast2go pipe
bali-phy	2.1.1	BAli-Phy is a Bayesian posterior sampler that employs Markov chain Monte Carlo to explore the joint space of alignment and phylogeny given molecular sequence data. Simultaneous estimation eliminates bias toward inaccurate alignment guide-trees, employs more sophisticated substitution models during alignment and automatically utilizes information in shared insertion/deletions to help infer phylogenies.
bam2fastq	1.1.0	There are a growing number of general-purpose SAM/BAM manipulation programs, including SAMtools, Picard, and Bamtools. This tool is not intended to duplicate the complex suite of tasks those programs perform. Rather, it is simply intended to extract raw sequences (with qualities). We envision this tool being primarily useful to those wishing to duplicate or extend previous analyses.
bamtools	0.9.0, 2.3.0	BamTools is a project that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating BAM (genome alignment) files.
bcbio-nextgen	0.6.5	A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. You write a high level configuration file specifying your inputs and analysis parameters. This input drives a parallel pipeline that handles distributed execution, idempotent processing restarts and safe transactional steps. The goal is to provide a shared community resource that handles the data processing component of sequencing analysis, providing researchers with more time to focus on the downstream biology.
bedtools	2.10.0, 2.10.1, 2.17.0	Collectively, the bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The most widely-used tools enable genome arithmetic: that is, set theory on the genome. For example, bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF.
biodatabase	1.0	Scripts to create, delete, and manage mysql databases on IGB's biodatabase server
blast+	2.2.25+, 2.2.28+	adds environmental variables to qiime and qiime
blast-intel	2.2.26	The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
blast	2.2.26	adds environmental variables to qiime and qiime
blat	0.34	adds environmental variables to blat
boost-intel	1.54	Boost provides free peer-reviewed portable C++ source libraries.
boost	1.54	Boost provides free peer-reviewed portable C++ source libraries.
bowtie	0.12.8, 0.12.9, 1.0.0	Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome at a rate of over 25 million 35-bp reads per hour. Bowtie indexes the genome with a Burrows-Wheeler index to keep its memory footprint small: typically about 2.2 GB for the human genome (2.9 GB for paired-end).
bowtie2	2.0.0-beta6, 2.0.2, 2.0.5, 2.1.0	adds environmental variables to Bowtie2
breseq	0.24	{Determine mutations in evolved microbes from next-generation sequencing data.
bwa	0.5.9, 0.7.5a	bio-bwa.sourceforge.net BWA is a software package for mapping low-divergent sequences against a large reference genome, such as the human genome
cafe	3.0	adds environmental variables to cafe
casava	1.8.2	adds environmental variables to casava
cdbfasta	0.99	fast indexing and retrieval of fasta records from flat file databases.
chance	1.0	CHANCE - CHip-seq ANalytics and Confidence Estimation. songlab.ucsf.edu/Software.html
chimera	1.5.3, 1.6.2	adds environmental variables for chimera
ClonalFrame	1.2	adds environmental variables to ClonalFrame
clustalw	2.1	adds environmental variables to clustalw
cufflinks	1.3.0, 2.1.1, 2.2.0	adds environmental variables to cufflinks
cytoscape	2.8.1, 2.8.3	adds environmental variables to cytoscape
deconseq	0.4.3	The DeconSeq tool can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
EagleView	2.2	adds environmental variables to EagleView
efiest	alpha	adds environmental variables for EFI QUEST alpha branch
emacs	24.3	Homepage:
EMBOSS	6.5.7	adds environmental variables to EMBOSS
erange	3.2.1, 3.3.0	A package of python scripts designed to analyze ultra-high-througphut sequencing data from the Illumina/Solexa platform for RNA-seq and ChIP-seq in metazoan genomes. The RNA-seq portion of ERANGE is described in our Nature Methods paper 'Mapping and quantifying mammalian transcriptomes by RNA-Seq' (Mortazavi, 2008). ERANGE is built on top of Cistematic.
fasta	36.3.5d	adds environmental variables to qiime and qiime
fasta_splitter	1	Description of the module
fastqc	0.10.1	adds environmental variables to fastqc
fastsimcoal2	1.1.1	fast sequential Markov coalescent simulation of genomic data under complex evolutionary models.
fasttree	2.1.7	FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7
ffmpeg	2.1.3	FFmpeg is a complete, cross-platform solution to record, convert and stream audio and video. It includes libavcodec - the leading audio/video codec library
findpeaks	3.1.9.2	adds environmental variables to findpeaks
flexbar	2.5-beta	Flexbar — flexible barcode and adapter removal, version 2.4
gams	24.2	The General Algebraic Modeling System (GAMS) is a high-level modeling system for mathematical programming and optimization. It consists of a language compiler and a stable of integrated high-performance solvers. GAMS is tailored for complex, large scale modeling applications, and allows you to build large maintainable models that can be adapted quickly to new situations.
gatk	1.6-13, 2.5-2, 2.6-4	The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
gcc	4.8.1	The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, Ada, and Go, as well as libraries for these languages (libstdc++, libgcj,...). GCC was originally written as the compiler for the GNU operating system. The GNU system was developed to be 100% free software, free in the sense that it respects the user's freedom.
gdal	1.10.1	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.
geneid	1.0	adds environmental variables to geneid
genomer	0.0.10	adds environmental variables to usearch
genometools	1.5.1, 1.5.2	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.
gff	2.1	Description of the module
glimmer	3.02	adds environmental variables to bedtools
gmap	2011-09-14, 2013-03-31	adds environmental variables to gmap and gsnap
gmes	v2.3e	adds environmental variables to gmes
gnuplot	4.6.3	Description of the module: Gnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms
graphviz	2.32.0	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.
gsl	1.16	The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.
hapcompass	0.7.5	HAPCOMPASS: A fast cycle basis algorithm for accurate haplotype assembly of sequence data
hdf4	4.2.10	HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. There are two versions of HDF: HDF4 and HDF5. HDF4 is the first HDF format. Although HDF4 is still funded, new users that are not constrained to using HDF4, should use HDF5 .
hdf5	1.8.11	HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. HDF5 is portable and is extensible, allowing applications to evolve in their use of HDF5. The HDF5 Technology suite includes tools and applications for managing, manipulating, viewing, and analyzing data in the HDF5 format.
hmmer-mpi	2.32-MPI-0.92	adds environmental variables to hmmer-mpi
hmmer	2.3.2, 3.0, 3.1	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). -
htseq	0.5.4, 0.6.1	HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
icc	2013.5.192	Intel® Parallel Studio XE 2013 SP1 provides C/C++ and Fortran developers cutting edge performing compilers and libraries, the right parallel programming models, and complementary and compatible analysis tools.
idba-ud	1.1.1	adds environmental variables to idba-ud
IGVTools	2.1.24	adds environmental variables to qiime and qiime
IMAGE	2.33	adds environmental variables to IMAGE
ImageMagick	6.7.8-9	ImageMagick® is a software suite to create, edit, compose, or convert bitmap images. It can read and write images in a variety of formats (over 100) including DPX, EXR, GIF, JPEG, JPEG-2000, PDF, PhotoCD, PNG, Postscript, SVG, and TIFF. Use ImageMagick to resize, flip, mirror, rotate, distort, shear and transform images, adjust image colors, apply various special effects, or draw text, lines, polygons, ellipses and Bézier curves.
infernal	1.1rc1, 1.1rc2	adds environmental variables to infernal 1.1 rc1
iprscan	4.8, 5.44, 5.45	InterProScan is a bioinformatics tool that provides a one-stop-shop for automated sequence analysis of both protein and nucleic acid, the latter via a full six-frame translation. It offers the ability to identify both structural and functional regions of interest, based upon methods and models that have been generated by a large number of member groups ('member databases').
issac	l.0.6	Isaac: Ultra-fast whole genome secondary analysis on Illumina sequencing platform
JAGS	3.4.0	JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation not wholly unlike BUGS. JAGS was written with three aims in mind:
java	1.6.0_41, 1.7.0_06-i386, 1.7.0_21, 1.7.0_55	adds environmental variables to java
jellyfish	1.1.6, 1.1.11	JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the 'compare-and-swap' CPU instruction to increase parallelism.
kmergenie	1.5854	Description of the module
krona	2.2	adds environmental variables to qiime and qiime
lamarc	2.1.8	adds environmental variables to cufflinks
last	278	Finds similar regions between sequences.
lastz	1.02.00	adds environmental variables to lastz
libstree	0.4.2	libstree is a generic suffix tree implementation, written in C. It can handle arbitrary data structures as elements of a string. Unlike most demo implementations, it is not limited to simple ASCII character strings.
libxml2	2.9.1	Libxml2 is the XML C parser and toolkit developed for the Gnome project (but usable outside of the Gnome platform), it is free software available under the MIT License.
LR-TRIRLS	20060531	LR-TRIRLS stands for Logistic Regression with Truncated Regularized Iteratively Re-weighted Least Squares. This is our contribution to LR computation.
lua	5.1.4, 5.2.2	adds environmental variables to lua
MACS	2.0.10	Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites.
mafft	6.953, 7.130	adds environmental variables to mafft
matlab-runtime	r2012b	http://www.mathworks.com/products/compiler/mcr/ The MATLAB Compiler Runtime (MCR) is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed
matlab	7.11.0.584	adds environmental variables to matlab
mcl	12-068	adds environmental variables to orthomcl
MEGAN	4.70.4, 5.1.0	In metagenomics, the aim is to understand the composition and operation of complex microbial consortia in environmental samples through sequencing and analysis of their DNA. Similarly, metatranscriptomics and metaproteomics target the RNA and proteins obtained from such samples.
meme	4.9.0	adds environmental variables to smrtanalysis-1.4.0
MetaGeneMark	2010	adds environmental variables to MetaGeneMark
metAMOS	1.2	metAMOS is an integrated assembly and analysis pipeline for metagenomic data. It is built around the Bambus2 metagenomic scaffolder and includes many current tools for assembly, gene finding, and taxonomic classification.
MetaVelvet	1.2.02, 1.2.02-kmer245	adds environmental variables to MetaVelvet
mira	3.2.1	adds environmental variables to mira
MOCAT	1.1	adds environmental variables for MOCAT
ModalClust	0.2, 0.3	adds environmental variables to ModalClust
mothur	1.28.0, 1.31.2, 1.32.0, 1.32.1	This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.
MotifScan	6	Swan Motif Scanning Software
mpich	3.0.4	MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
mpich2	1.4.1p1, 1.5	MPICH is a high performance and widely portable implementation of the Message Passing Interface (MPI) standard.
msort	1.0	adds environmental variables to msort
muscle	3.8.31	adds environmental variables to velvet
nco	4.4.2	NCO manipulates data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. It also exploits the geophysical expressivity of many CF (Climate & Forecast) metadata conventions, the flexible description of physical dimensions translated by UDUnits, the network transparency of OPeNDAP, the storage features (e.g., compression, chunking, groups) of HDF (the Hierarchical Data Format), and many powerful mathematical and statistical algorithms of GSL (the GNU Scientific Library). NCO is fast, powerful, and free.
novocraft	2.08, 2.08.02, 2.08.03, 3.00.02, 3.00.05, 3.02	adds environmental variables to novocraft
oases-kmer245	0.2.8	Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
oases	0.2.8	Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.
ocaml	4.01	Ocaml Compiler
OLB	1.9.4	adds environmental variables to qiime and qiime
openmpi-intel	1.6.3	The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
openmpi	1.6.3	The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
orthomcl	2.0.2, 2.0.7	adds environmental variables to orthomcl
paml	4.4	adds environmental variables to paml
parallel-netcdf	1.4.1	Parallel netCDF (PnetCDF) is an I/O library that supports data access to netCDF files in parallel, a collaborative work of Northwestern University and Argonne National Laboratory.
parallel	20121122	adds environmental variables to orthomcl
PBJelly	12.9.14	adds environmental variables to PBJelly with smrtanalysis-1.4.0
peaksplitter	1.0	adds environmental variables to peaksplitter
perfsuite	1.0.0	adds environmental variables to perfsuite
perl	5.16.1	Perl 5 is a highly capable, feature-rich programming language with over 25 years of development. Perl 5 runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
phred	0.020425.c	adds environmental variables to qiime and qiime
phylip	3.69	adds environmental variables to phylip
phylocsf	may-16-2014	Phylogenetic analysis of multi-species genome sequence alignments to identify conserved protein-coding region
phymmbl	4.0	adds environmental variables to phymmbl
picard-tools	1.34, 1.73	adds environmental variables to picard-tools
polyphen	2.2.2	PolyPhen-2 (Polymorphism Phenotyping v2) is a software tool which predicts possible impact of amino acid substitutions on the structure and function of human proteins using straightforward physical and evolutionary comparative considerations.
pplacer	1.0, 1.1	adds environmental variables to pplacer
prank	121002	adds environmental variables to prank
prinseq	0.20.4	PRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data. It generates summary statistics of your sequences in graphical and tabular format. It is easily configurable and provides a user-friendly interface.
prodigal	2.0, 2.2	adds environmental variables to prodigal
proj	4.8.0	Program proj (release 3) is a standard Unix filter function which converts ge-ographic longitude and latitude coordinates into cartesian coordinates, (λ,φ)→(x,y), by means of a wide variety of cartographic projection functions.
qiime	1.3.0, 1.5.0, 1.6.0, 1.7.0	Loads qiimes environmental variables
quake	0.3.4	Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
quest	alpha, devel	adds environmental variables for EFI QUEST development branch
R	2.15.0, 2.15.1, 2.15.2, 3.0.0, 3.0.2	R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R.
RAxML	7.3.0	RAxML (Randomized Axelerated Maximum Likelihood) is a program for sequential and parallel Maximum Likelihood based inference of large phylogenetic trees. It has originally been derived from fastDNAml which in turn was derived from Joe Felsentein’s dnaml which is part of the PHYLIP package.
ray	2.20, 2.30	Ray -- Parallel genome assemblies for parallel DNA sequencing denovoassembler.sourceforge.net/index.html
rdp_classifier	2.5	The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
repeatmasker	3.28	RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences
rockhopper	1.2	Description of the module Rockhopper, Rockhopper is a comprehensive and user-friendly system for computational analysis of bacterial RNA-seq data ttp://cs.wellesley.edu/~btjaden/Rockhopper/
rsa-tools	2012-10-09	adds environmental variables to qiime and qiime
ruby	1.9.3	adds environmental variables to ruby
sam_comp	0.7	adds environmental variables Python 2.7.3
SICER	1.1	A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
signalp	4.1	adds environmental variables to perl
smrtanalysis	1.4.0, 2.0.1	SMRT Analysis is a bioinformatics software suite for analyzing single molecule, real-time DNA sequencing data from Pacific Biosciences. This repository contains a link to download and view the SMRT Analysis source code. It is provided here for reference only and is currently not buildable.
SnpEff	3.2	Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
SOAP2	2.2	adds environmental variables to SOAP2
SOAPdenovo-Trans	1.02	SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.The assembler provides a more accurate, complete and faster way to construct the full-length transcript sets.
SOAPdenovo	2.04	adds environmental variables to SOAPdenovo
SOAPdenovo2	r240	adds environmental variables to SOAPdenovo2
SOAPec	2.01, 2.02	http://soap.genomics.org.cn/about.html
SOAPErrorCorrection	0.04	adds environmental variables to SOAPErrorCorrection
SOAPGapCloser	1.12	adds environmental variables to SOAPGapCloser
SOAPprepare	0.1	adds environmental variables to SOAPdenovo
spades	3.0.0	Homepage:
speciateit	184	This is a beta version of a speciation pipeline for 16S rRNA amplicon data. In principle, the pipeline can be used for speciation based on any highly preserved gene.
speciate_it	184	This is a beta version of a speciation pipeline for 16S rRNA amplicon data. In principle, the pipeline can be used for speciation based on any highly preserved gene.
sratoolkit	2.1.16	adds environmental variables to sratoolkit
srna-tools	20130118	adds environmental variables to srna-tools
tabix	0.2.6	Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file in.tab.bgz.tbi when region is absent from the command-line.
tbb	4.2-3	Intel® Threading Building Blocks (Intel® TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable and composable, and that have future-proof scalability.
tcoffee	10-r1613	A collection of tools for Computing, Evaluating and Manipulating Multiple Alignments of DNA, RNA, Protein Sequences and Structures
tmhmm	2.0	Prediction of transmembrane helices in proteins
tophat	1.4.1	TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
tophat2	2.0.4, 2.0.5, 2.0.6, 2.0.7, 2.0.8, 2.0.10	TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
treemix	1.12	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	4.04	Tandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
trimmomatic	0.22, 0.27, 0.30	Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.
trinityrnaseq-intel	r2013-02-25, r2014-04-13	Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
trinityrnaseq	r2014-04-13	Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
truesight	0.06	Self-training Algorithm for Splice Junction Detection using RNA-seq.
uchime	4.2.40	UCHIME is an algorithm for detecting chimeric sequences. It is implemented in the uchime_ref and uchime_denovo commands.
usearch	4.2.66	USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
vcftools	0.1.11	VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
VelvetOptimiser	2.2.5	VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
yasm	1.2.0	Yasm is a complete rewrite of the NASM assembler under the 'new' BSD License (some portions are under other licenses, see COPYING for details). Yasm currently supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes, outputs binary, ELF32, ELF64, 32 and 64-bit Mach-O, RDOFF2, COFF, Win32, and Win64 object formats, and generates source debugging information in STABS, DWARF 2, and CodeView 8 formats

Difference between revisions of "Biocluster Applications"

Revision as of 02:26, 28 May 2014

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 |20110922
 |ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated sequencing data. ART can also simulate reads using user own read error model or quality profiles.
-|-
-|[https://www.sanger.ac.uk/resources/software/artemis/ artemis]
-|14.0
-|Artemis is a free genome browser and annotation tool that allows visualisation of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation.
 |-
 |[http://bioinf.uni-greifswald.de/augustus/ augustus]
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 |2.5
 |adds environmental variables to blast2go pipe
-|-
-|babraham
-|bioinformatics
-|Description of the module
 |-
 |[http://www.bali-phy.org/ bali-phy]
@@ Line 76: / Line 68: @@
 |1.0
 |Scripts to create, delete, and manage mysql databases on IGB's biodatabase server
-|-
-|biopieces
-|0.48
-|adds environmental variables, software, and bins to biopieces
 |-
 |blast+
@@ Line 92: / Line 80: @@
 |2.2.26
 |adds environmental variables to qiime and qiime
-|-
-|blast2go
-|2.5
-|Description of the module
 |-
 |blat
@@ Line 126: / Line 110: @@
 |-
 |cafe
-|2.2, 3.0
+|3.0
 |adds environmental variables to cafe
 |-
@@ Line 132: / Line 116: @@
 |1.8.2
 |adds environmental variables to casava
-|-
-|[http://weizhong-lab.ucsd.edu/cd-hit/ cd-hit]
-|4.6, 4.6.1
-|CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CD-HIT was originally developed by Dr. Weizhong Li at Dr. Adam Godzik's Lab at the Burnham Institute (now Sanford-Burnham Medical Research Institute)
 |-
 |[http://cdbfasta.sourceforge.net/ cdbfasta]
@@ Line 148: / Line 128: @@
 |1.5.3, 1.6.2
 |adds environmental variables for chimera
-|-
-|[http://www.biostat.jhsph.edu/~hji/cisgenome/ cisgenome]
-|2.0
-|An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis.
 |-
 |ClonalFrame
 |1.2
 |adds environmental variables to ClonalFrame
-|-
-|clustalo
-|1.2.0
-|Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make use of multiple processors, where present. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. clustal.org/omega
 |-
 |clustalw
 |2.1
 |adds environmental variables to clustalw
-|-
-|[http://www.cmake.org/cmake/resources/software.html cmake]
-|2.8.12.2
-|CMake, the cross-platform, open-source build system
 |-
 |cufflinks
-|1.1.0, 1.3.0, 2.0.2, 2.1.1, 2.2.0, 2.2.1
+|1.3.0, 2.1.1, 2.2.0
 |adds environmental variables to cufflinks
-|-
-|[https://code.google.com/p/cutadapt/ cutadapt]
-|1.2
-|cutadapt removes adapter sequences from high-throughput sequencing data. This is usually necessary when the read length of the sequencing machine is longer than the molecule that is sequenced, for example when sequencing microRNAs.
 |-
 |cytoscape
@@ Line 190: / Line 154: @@
 |-
 |efiest
-|alpha, devel
+|alpha
-|adds environmental variables for EFI QUEST development branch
+|adds environmental variables for EFI QUEST alpha branch
 |-
 |emacs
@@ Line 204: / Line 168: @@
 |3.2.1, 3.3.0
 |A package of python scripts designed to analyze ultra-high-througphut sequencing data from the Illumina/Solexa platform for RNA-seq and ChIP-seq in metazoan genomes. The RNA-seq portion of ERANGE is described in our Nature Methods paper 'Mapping and quantifying mammalian transcriptomes by RNA-Seq' (Mortazavi, 2008). ERANGE is built on top of Cistematic.
-|-
-|[http://estscan.sourceforge.net/ estscan]
-|3.0.3
-|ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts.
 |-
 |fasta
@@ Line 228: / Line 188: @@
 |2.1.7
 |FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. For large alignments, FastTree is 100-1,000 times faster than PhyML 3.0 or RAxML 7
-|-
-|fastx_toolkit
-|0.0.13
-|adds environmental variables to fastx_toolkit
 |-
 |[http://www.ffmpeg.org/index.html ffmpeg]
@@ Line 244: / Line 200: @@
 |2.5-beta
 |Flexbar — flexible barcode and adapter removal, version 2.4
-|-
-|freebayes
-|0.9.6
-|adds environmental variables to freebayes
 |-
 |[http://www.gams.com/ gams]
@@ Line 254: / Line 206: @@
 |-
 |[http://www.broadinstitute.org/gatk gatk]
-|1.6-5, 1.6-13, 2.5-2, 2.6-4
+|1.6-13, 2.5-2, 2.6-4
 |The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
 |-
@@ Line 284: / Line 236: @@
 |3.02
 |adds environmental variables to bedtools
-|-
-|[https://www.globus.org/ globusconnect]
-|1.6
-|Allows you to use globus connect 1.6 to transfer files on globus
 |-
 |gmap
@@ Line 338: / Line 286: @@
 |-
 |idba-ud
-|1.1.0, 1.1.1
+|1.1.1
 |adds environmental variables to idba-ud
-|-
-|IGV
-|2.1.24
-|adds environmental variables to IGV
 |-
 |IGVTools
@@ Line 360: / Line 304: @@
 |1.1rc1, 1.1rc2
 |adds environmental variables to infernal 1.1 rc1
-|-
-|inparanoid
-|4.1
-|adds environmental variables for inparanoid
 |-
 |[http://code.google.com/p/interproscan/ iprscan]
@@ Line 378: / Line 318: @@
 |-
 |java
-|1.6.0_41, 1.7.0_06-i386, 1.7.0_07, 1.7.0_21, 1.7.0_55
+|1.6.0_41, 1.7.0_06-i386, 1.7.0_21, 1.7.0_55
 |adds environmental variables to java
 |-
@@ Line 384: / Line 324: @@
 |1.1.6, 1.1.11
 |JELLYFISH is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. JELLYFISH can count k-mers using an order of magnitude less memory and an order of magnitude faster than other k-mer counting packages by using an efficient encoding of a hash table and by exploiting the 'compare-and-swap' CPU instruction to increase parallelism.
-|-
-|khmer
-|2013-05-06
-|adds environmental variables khmer
 |-
 |kmergenie
@@ Line 426: / Line 362: @@
 |-
 |[http://liulab.dfci.harvard.edu/MACS/ MACS]
-|1.4.2, 2.0.10
+|2.0.10
 |Next generation parallel sequencing technologies made chromatin immunoprecipitation followed by sequencing (ChIP-Seq) a popular strategy to study genome-wide protein-DNA interactions, while creating challenges for analysis algorithms. We present Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites.
 |-
@@ Line 464: / Line 400: @@
 |1.2.02, 1.2.02-kmer245
 |adds environmental variables to MetaVelvet
-|-
-|mfinder
-|1.2
-|adds environmental variables to mfinder
 |-
 |mira
@@ Line 482: / Line 414: @@
 |-
 |[http://www.mothur.org/ mothur]
-|1.8, 1.28.0, 1.31.2, 1.32.0, 1.32.1
+|1.28.0, 1.31.2, 1.32.0, 1.32.1
 |This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. We have incorporated the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and much more. In addition to improving the flexibility of these algorithms, we have added a number of other features including calculators and visualization tools.
 |-
@@ Line 500: / Line 432: @@
 |1.0
 |adds environmental variables to msort
-|-
-|MUMmer
-|3.23
-|adds environmental variables to MUMmer
 |-
 |muscle
@@ Line 512: / Line 440: @@
 |4.4.2
 |NCO manipulates data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. It also exploits the geophysical expressivity of many CF (Climate & Forecast) metadata conventions, the flexible description of physical dimensions translated by UDUnits, the network transparency of OPeNDAP, the storage features (e.g., compression, chunking, groups) of HDF (the Hierarchical Data Format), and many powerful mathematical and statistical algorithms of GSL (the GNU Scientific Library). NCO is fast, powerful, and free.
-|-
-|[http://www.unidata.ucar.edu/software/netcdf/ netcdf]
-|4.3.1.1
-|NetCDF is a set of software libraries and self-describing, machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
 |-
 |novocraft
-|2.08, 2.08.02, 2.08.03, 3.00.01, 3.00.02, 3.00.05, 3.02
+|2.08, 2.08.02, 2.08.03, 3.00.02, 3.00.05, 3.02
 |adds environmental variables to novocraft
 |-
@@ Line 536: / Line 460: @@
 |1.9.4
 |adds environmental variables to qiime and qiime
-|-
-|[http://opam.ocaml.org opam]
-|1.1.1
-|Package manager for OCaml
 |-
 |[http://www.open-mpi.org/ openmpi-intel]
@@ Line 546: / Line 466: @@
 |-
 |[http://www.open-mpi.org/ openmpi]
-|1.4.3, 1.6.3
+|1.6.3
 |The Open MPI Project is an open source MPI-2 implementation that is developed and maintained by a consortium of academic, research, and industry partners.
 |-
@@ Line 564: / Line 484: @@
 |20121122
 |adds environmental variables to orthomcl
-|-
-|pathway-tools
-|16.5
-|adds environmental variables to pathway-tools
 |-
 |PBJelly
@@ Line 584: / Line 500: @@
 |5.16.1
 |Perl 5 is a highly capable, feature-rich programming language with over 25 years of development. Perl 5 runs on over 100 platforms from portables to mainframes and is suitable for both rapid prototyping and large scale development projects.
-|-
-|[ftp://ftp.sanger.ac.uk/pub/databases/Pfam/Tools/ pfamscan]
-|1.0
-|PFamscan
 |-
 |phred
@@ Line 606: / Line 518: @@
 |-
 |picard-tools
-|1.34, 1.73, 1.90
+|1.34, 1.73
 |adds environmental variables to picard-tools
 |-
@@ Line 632: / Line 544: @@
 |4.8.0
 |Program proj (release 3) is a standard Unix filter function which converts ge-ographic longitude and latitude coordinates into cartesian coordinates, (λ,φ)→(x,y), by means of a wide variety of cartographic projection functions.
-|-
-|python
-|2.6.6, 2.7.3, 2.7.3-sqlite, 2.7.5-galaxy, 3.2.3
-|adds environmental variables to Python 3.2
 |-
 |qiime
-|1.3.0, 1.5.0, 1.6.0, 1.7.0, 1.8.0
+|1.3.0, 1.5.0, 1.6.0, 1.7.0
 |Loads qiimes environmental variables
 |-
@@ Line 644: / Line 552: @@
 |0.3.4
 |Quake is a package to correct substitution sequencing errors in experiments with deep coverage (e.g. >15X), specifically intended for Illumina sequencing reads.
-|-
-|[http://bioinf.spbau.ru/quast quast]
-|2.2
-|QUAST evaluates genome assemblies.  It can works both with and without a given reference genome.  The tool accepts multiple assemblies, thus is suitable for comparison.
 |-
 |quest
@@ Line 668: / Line 572: @@
 |2.5
 |The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment.
-|-
-|rdxplorer
-|3.2
-|adds environmental variables rdexplorer. use 'python rdxplorer.py to run'
 |-
 |repeatmasker
@@ Line 684: / Line 584: @@
 |2012-10-09
 |adds environmental variables to qiime and qiime
-|-
-|rstudio
-|0.97.312
-|adds environmental variables to R
 |-
 |ruby
 |1.9.3
 |adds environmental variables to ruby
-|-
-|[http://samtools.sourceforge.net/ samtools]
-|0.1.16, 0.1.18, 0.1.19
-|SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
 |-
 |sam_comp
@@ Line 714: / Line 606: @@
 |-
 |[http://snpeff.sourceforge.net/ SnpEff]
-|3.2, 3.3e
+|3.2
 |Genetic variant annotation and effect prediction toolbox. It annotates and predicts the effects of variants on genes (such as amino acid changes).
 |-
@@ Line 768: / Line 660: @@
 |20130118
 |adds environmental variables to srna-tools
-|-
-|[https://www.sanger.ac.uk/resources/software/ssaha/ ssaha2]
-|2.5.5
-|SSAHA is a software tool for very fast matching and alignment of DNA sequences.  It achieves its fast search speed by converting sequence information into a 'hash table' data structure, which can then be searched very rapidly for matches.
-|-
-|[http://www.baseclear.com SSPACE-premium]
-|2.3.1
-|SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired end libraries, or even a combination.
-|-
-|[http://www.baseclear.com SSPACE]
-|1.1
-|SSPACE is a script able to extend and scaffold pre-assembled contigs using one or more mate pairs or paired end libraries, or even a combination.
-|-
-|[http://creskolab.uoregon.edu/stacks/ stacks]
-|0.9996, 0.99994
-|Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform.
-|-
-|[http://pritchardlab.stanford.edu/structure.html structure]
-|2.3.4
-|The program structure is a free software package for using multi-locus genotype data to investigate population structure. Its uses include inferring the presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed.
-|-
-|[http://subread.sourceforge.net/ subread]
-|3.1.6
-|The Subread package comprises a suite of software programs for processing next-gen sequencing read data including:
-|-
-|[http://supfam.org/SUPERFAMILY/ supfam]
-|1.75
-|SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes.
 |-
 |[http://samtools.sourceforge.net/tabix.shtml tabix]
@@ Line 838: / Line 702: @@
 |-
 |[http://trinityrnaseq.sourceforge.net/ trinityrnaseq]
-|r2012-06-08, r2013-02-25, r2013-08-14, r2014-04-13
+|r2014-04-13
 |Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data.
-|-
-|[http://trinotate.sourceforge.net/ trinotate]
-|r20130826
-|Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
 |-
 |[http://bioen-compbio.bioen.illinois.edu/TrueSight/ truesight]
@@ Line 852: / Line 712: @@
 |4.2.40
 |UCHIME is an algorithm for detecting chimeric sequences. It is implemented in the uchime_ref and uchime_denovo commands.
-|-
-|[http://www.unidata.ucar.edu/software/udunits/ udunits]
-|2.1.24
-|The UDUNITS package supports units of physical quantities. Its C library provides for arithmetic manipulation of units and for conversion of numeric values between compatible units. The package contains an extensive unit database, which is in XML format and user-extendable. The package also contains a command-line utility for investigating units and converting values.
 |-
 |[http://www.drive5.com/usearch/ usearch]
-|4.2.66, 6.0.307, 6.1.544, 7.0.959
+|4.2.66
 |USEARCH is a unique sequence analysis tool with thousands of users world-wide. USEARCH offers search and clustering algorithms that are often orders of magnitude faster than BLAST.
-|-
-|[http://useq.sourceforge.net/ USeq]
-|8.5.1
-|USeq is a collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms.
 |-
 |[http://vcftools.sourceforge.net/ vcftools]
-|0.1.7, 0.1.11
+|0.1.11
 |VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
-|-
-|[http://www.ebi.ac.uk/~zerbino/velvet/ velvet-kmer245]
-|1.2.10
-|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.ebi.ac.uk/~zerbino/velvet/ velvet]
-|1.1.04, 1.2.08, 1.2.10
-|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.
 |-
 |[http://bioinformatics.net.au/software.velvetoptimiser.shtml VelvetOptimiser]
 |2.2.5
 |VelvetOptimiser is a multi-threaded Perl script for automatically optimising the three primary parameter options (K, -exp_cov, -cov_cutoff) for the Velvet de novo sequence assembler.
-|-
-|[http://vim.org vim]
-|7.4
-|Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set. It's useful whether you're already using vi or using a different editor.
-|-
-|[http://www.ncbi.nlm.nih.gov/pubmed/23413434 wessim]
-|1.0
-|A whole-exome sequencing simulator based on in silico exome capture
-|-
-|[https://www.ebi.ac.uk/Tools/sss/fasta/wgs.html wgs]
-|7.0
-|This tool provides sequence similarity searching against the EMBL (WGS) database using the FASTA suite of programs.
-|-
-|[https://wiki.gacrc.uga.edu/wiki/WISE2 wise]
-|2.2.3-rc7
-|Wise2 has four main executable programs using sequence inputs which are designed to provide access to the main algorithms sensibly. The algorithms you are interested in is genewise - compare protein information to genomic DNA and estwise - compare protein information to EST/cDNA DNA.
 |-
 |[http://yasm.tortall.net/ yasm]
 |1.2.0
 |Yasm is a complete rewrite of the NASM assembler under the 'new' BSD License (some portions are under other licenses, see COPYING for details).  Yasm currently supports the x86 and AMD64 instruction sets, accepts NASM and GAS assembler syntaxes, outputs binary, ELF32, ELF64, 32 and 64-bit Mach-O, RDOFF2, COFF, Win32, and Win64 object formats, and generates source debugging information in STABS, DWARF 2, and CodeView 8 formats
-|-
-|[http://www.zlib.net/ zlib]
-|1.2.8
-|zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. The zlib data format is itself portable across platforms.
 |}