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Module prerequisites

If a module lists one or more prerequisites, the prerequisite module(s) must be loaded before or along with, that module.

For example, the cdo/2.1 modules requires compiler/pgi/13. To load the cdo module, doing either

module load compiler/pgi/13
module load cdo/2.1

or

module load compiler/pgi/13 cdo/2.1 (Note the prerequisite module must be first.)

is acceptable.

Multiple versions

Some packages list multiple compilers for prerequisites. This means that the package has been built with each version of the compilers listed.

NameVersionModule NamePrerequisitesTypeDomainDescription
abacus1.0.1abacus/1.0compiler/intel/13:openmpi/1.8 libraryruntime support
abayesqr1.0abayesqr/1.0None applicationhigh-throughput sequencing dataaBayesQR is a viral quasispecies reconstruction algorithm that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data.
abinit8.0.8abinit/8.0compiler/intel/12:openmpi/1.8 applicationcomputational chemistryABINIT is a package whose main program allows one to find the total energy.
abinit8.4.2abinit/8.4compiler/intel/15:openmpi/1.10 applicationcomputational chemistryABINIT is a package whose main program allows one to find the total energy.
afterqc0.9.0afterqc/0.9None applicationpackageAfterQC can simply go through all fastq files in a folder and then output three folders: good, bad and QC folders, which contains good reads, bad reads and the QC results of each fastq file/pair.
allinea4.2allinea/4.2None applicationUtility
allinea5.0allinea/5.0None applicationUtility
allinea5.1allinea/5.1None applicationUtility
allinea6.0allinea/6.0None applicationUtility
allinea6.1allinea/6.1None applicationUtility
allinea7.0allinea/7.0None applicationUtility
allpathslgLatestallpathslg/latestcompiler/gcc/4.7 applicationbiology
anaconda2.7anaconda/2.7None applicationsystem
anaconda3.3anaconda/3.3None applicationsystem
anaconda3.4anaconda/3.4None applicationsystem
anaconda4.3anaconda/4.3None applicationsystem
ant1.10ant/1.10None libraryjava
ant1.9ant/1.9None libraryjava
aria21.23.0aria2/1.23None applicationtoolaria2 is a lightweight multi-protocol & multi-source command-line download utility.
art2.6.0art/2.6None applicationcomputational biologyART is a set of simulation tools to generate synthetic next-generation sequencing reads.
asreml3.0asreml/3.0None applicationdata analysisASReml
asreml4.1asreml/4.1None applicationdata analysisASReml
atk13.8.2atk/13.8.2compiler/gcc/4.7:mpich2/1.5 applicationChemistry
atk2014.1atk/2014.1compiler/gcc/4.7:mpich2/1.5 applicationChemistry
atk2015.1atk/2015.1compiler/gcc/4.7:mpich2/1.5 applicationChemistry
augustus3.0augustus/3.0compiler/gcc/4.9 None applicationcomputational biologyAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
augustus3.2.3augustus/3.2None applicationcomputational biologyAUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
autoconf2.69autoconf/2.69None applicationUtilitiesAutoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages.
automake1.14automake/1.14None applicationUtilitiesAutomake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
automake1.15automake/1.15None applicationUtilitiesAutomake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
awscli1.1.120awscli/1.11None applicationutilityThe AWS CLI is an open source tool built on top of the AWS SDK for Python (Boto) that provides commands for interacting with AWS services.
ballgown2.2.0ballgown/2.2None applicationcomputational biologyBallgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly.
bam-readcount0.6bam-readcount/0.6None applicationcomputational biologyThe purpose of this program is to generate metrics at single nucleotide positions.
bamtools2.3bamtools/2.3None applicationcomputational biologyBamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
bayespeak1.24.0bayespeak/1.24.0None applicationcomputational biologyThis package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.
bbmap37.17bbmap/37.17None applicationcomputational biologyBBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bcftools1.1bcftools/1.1compiler/gcc/4.8 applicationcomputational biologyBCF Tools - a generic tool for the Variant Call Format(VCF)
bcftools1.2bcftools/1.2compiler/gcc/4.8 applicationcomputational biologyBCF Tools - a generic tool for the Variant Call Format(VCF)
bcftools1.3.1bcftools/1.3None applicationcomputational biologybcftools — utilities for variant calling and manipulating VCFs and BCFs.
bcl2fastq1.8.4bcl2fastq/1.8None applicationbiologybcl2fastq can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis
bcl2fastq2.17bcl2fastq/2.17compiler/gcc/4.7 applicationbiologybcl2fastq can be used to demultiplex data and convert BCL files to FASTQ file formats for downstream analysis
beagle4.1_21Jan17beagle/4.1None applicationBiologyBeagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beast1.8beast/1.8None applicationbiologyBEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
beast22.4beast2/2.4None applicationbiologyBEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
bedtools2.24bedtools/2.24None applicationcomputational biologybedtools: a powerful toolset for genome arithmetic.
beta1.0.7beta/1.0None applicationcomputational biologyBinding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
BICseq1.1.2BICseq/1.1None applicationcomputational biologyBIC-seq can accurately and efficiently identify CNVs via minimizing the Bayesian information criterion.
bioconductor3.4bioconductor/3.4None applicationcomputational biologyBioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
biodata1.0biodata/1.0None applicationcomputational biologyStatic data resources for bioinformatics/computational biology.
biom-format2.1biom-format/2.1None applicationcomputational biologyThe BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.
bioperl1.6bioperl/1.6None applicationcomputational biologyBioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications
biopieces1.0biopieces/1.0compiler/gcc/4.8:openmpi/1.6 applicationcomputational biologyThe Biopieces are a collection of bioinformatics tools that can be pieced together in a very easy and flexible manner to perform both simple and complex tasks.
biopython1.70biopython/1.70None librarybiological computationBiopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biosamtools1.38biosamtools/1.38None applicationcomputational biology
bismark0.14.2bismark/0.14None applicationcomputational biologyBisulfite read mapper and methylation caller.
blast2.2.29blast/2.2.29None applicationcomputational biologyNCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast2.2.30blast/2.2None applicationcomputational biologyNCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast2.4.0blast/2.4None applicationcomputational biologyNCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast-legacy2.2.26blast-legacy/2.2.26None applicationcomputational biologyNCBI BLAST sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blat35x1blat/35x1None applicationcomputational biologyBlat is an alignment tool like BLAST, but it is structured differently. On DNA, Blat works by keeping an index of an entire genome in memory. Thus, the target database of BLAT is not a set of GenBank sequences, but instead an index derived from the assembly of the entire genome.
boost1.44boost/1.44compiler/gcc/4.9 None applicationSystem Environment/BaseBoost provides free peer-reviewed portable C++ source libraries.
boost1.54boost/1.54compiler/gcc/4.9 applicationSystem Environment/BaseBoost provides free peer-reviewed portable C++ source libraries.
boost1.55boost/1.55compiler/gcc/4.9:openmpi/1.10 applicationSystem Environment/BaseBoost provides free peer-reviewed portable C++ source libraries.
boost1.55.0boost/1.55.0None applicationSystem Environment/BaseBoost provides free peer-reviewed portable C++ source libraries.
boost1.57boost/1.57compiler/gcc/4.9 applicationSystem Environment/BaseBoost provides free peer-reviewed portable C++ source libraries.
boost1.59boost/1.59compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 compiler/intel/13 applicationSystem Environment/BaseBoost provides free peer-reviewed portable C++ source libraries.
boost1.63boost/1.63compiler/gcc/6.1 compiler/intel/16 applicationSystem Environment/BaseBoost provides free peer-reviewed portable C++ source libraries.
boost1.64boost/1.64compiler/gcc/7.1 applicationSystem Environment/BaseBoost provides free peer-reviewed portable C++ source libraries.
bowtie1.0bowtie/1.0None applicationcomputational biologyUltrafast, memory-efficient short read aligner
bowtie1.1.2bowtie/1.1None applicationcomputational biologyUltrafast, memory-efficient short read aligner
bowtie2.2.6bowtie/2.2None applicationcomputational biologyUltrafast, memory-efficient short read aligner
breakdancer1.4breakdancer/1.4None applicationcomputational biologyBreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
bwa0.6.2bwa/0.6None applicationcomputational biologybwa - Burrows-Wheeler Alignment Tool
bwa0.7bwa/0.7None applicationcomputational biologybwa - Burrows-Wheeler Alignment Tool
bzip21.0bzip2/1.0None libraryruntime support
caffe1.0caffe/1.0None applicationpackageIt is developed by the Berkeley Vision and Learning Center (BVLC) and by community contributors. Yangqing Jia created the project during his PhD at UC Berkeley. Caffe is released under the BSD 2-Clause license.
cap3122107cap3/122107None applicationcomputational biologyCAP3: A DNA Sequence Assembly Program
carlsim3.1carlsim/3.1None applicationcomputational biologyCARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail.
carlsim4.0carlsim/4.0None applicationcomputational biologyCARLsim is an efficient, easy-to-use, GPU-accelerated software framework for simulating large-scale spiking neural network (SNN) models with a high degree of biological detail.
ccat3.0ccat/3.0None applicationcomputational biologyA software package for the analysis of ChIP-seq data with negative control.
ccp47.0ccp4/7.0None applicationunknown
cd-hit4.6cd-hit/4.6None applicationcomputational biologycd-hit is a very widely used program for clustering and comparing protein or nucleotide sequences.
cdo1.6cdo/1.6compiler/pgi/13 libraryruntime support
cdo1.7.1cdo/1.7compiler/intel/15 compiler/pgi/14 compiler/pgi/15 libraryruntime support
cdo1.8cdo/1.8compiler/pgi/13 libraryruntime support
cdo1.8.1cdo/1.8compiler/intel/15 compiler/intel/16 compiler/pgi/14 compiler/pgi/15 libraryruntime support
cexor1.10cexor/1.10None applicationcomputational biologyAn R package to uncover high-resolution protein-DNA interactions in ChIP-exo replicates.
clearcut1.0clearcut/1.0None applicationcomputational biologyClearcut - The reference implementation for Relaxed Neighbor Joining (RNJ)
clustal-omega1.2clustal-omega/1.2None applicationcomputational biologyClustal 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
clustalw2.1clustalw/2.1None applicationcomputational biologyClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences.
cmake2.8cmake/2.8None applicationunknown
cmake3.5cmake/3.5None applicationunknown
CNVnator0.3CNVnator/0.3compiler/gcc/4.9 applicationgenotypingCNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing.
compiler/gcc4.7compiler/gcc/4.7None applicationcompiler
compiler/gcc4.8compiler/gcc/4.8None applicationcompiler
compiler/gcc4.9compiler/gcc/4.9None applicationcompiler
compiler/gcc5.4compiler/gcc/5.4None applicationcompiler
compiler/gcc6.1compiler/gcc/6.1None applicationcompiler
compiler/gcc7.1compiler/gcc/7.1None applicationcompiler
compiler/intel12compiler/intel/12None applicationcompiler
compiler/intel13compiler/intel/13None applicationcompiler
compiler/intel15compiler/intel/15None applicationcompiler
compiler/intel16compiler/intel/16None applicationcompiler
compiler/pgi12compiler/pgi/12None applicationcompiler
compiler/pgi13compiler/pgi/13None applicationcompiler
compiler/pgi14compiler/pgi/14None applicationcompiler
compiler/pgi15compiler/pgi/15None applicationcompiler
compiler/pgi16compiler/pgi/16None applicationcompiler
cp2k2.6cp2k/2.6compiler/gcc/4.7:openmpi/1.8 libraryruntime support
cp2k3.0cp2k/3.0compiler/gcc/4.7:openmpi/1.8 libraryruntime support
crest1.0crest/1.0None applicationcomputational biology
csaw1.4csaw/1.4None applicationcomputational biologyDetection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.
cuda6.0cuda/6.0None applicationcompilerNVIDIA CUDA Toolkit for Linux.
cuda6.5cuda/6.5None applicationcompilerNVIDIA CUDA Toolkit for Linux.
cuda7.5cuda/7.5None applicationcompilerNVIDIA CUDA Toolkit for Linux.
cuda8.0cuda/8.0None applicationcompilerNVIDIA CUDA Toolkit for Linux.
cudnnv5cudnn/v5None applicationcompilerNVIDIA cuDNN Toolkit for Linux.
cufflinks2.1cufflinks/2.1None applicationcomputational biologycufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq
cufflinks2.2cufflinks/2.2None applicationcomputational biologycufflinks - Transcript assembly, differential expression, and differential regulation for RNA-Seq
curl7.50curl/7.50None applicationnetwork
cutadapt1.13cutadapt/1.13None applicationNGS dataCutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutadapt1.4cutadapt/1.4None applicationcomputational biologyCutadapt removes adapter sequences from DNA high-throughput sequencing data.
deap1.0deap/1.0None applicationcomputer scienceDEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas.
diffsplice0.1.11diffsplice/0.1None applicationcomputational biologyDiffSplice: the Genome-Wide Detection of Differential Splicing Events with RNA-seq
dmtcp2.0dmtcp/2.0None applicationUtility
dmtcp2.3dmtcp/2.3None applicationUtility
dmtcp2.4dmtcp/2.4None applicationUtility
dmtcp2.5dmtcp/2.5None applicationUtility
ea-utils1.01ea-utils/1.0None applicationcomputational biologyEA Utils is a collection of command line tools for processing NextGen sequencing data. Included are fastq-stats and sam-stats which are lightweight tools that display a variety of statistics on fastq and sam files.
elk4.3.6elk/4.3compiler/intel/13:openmpi/1.8 libraryruntime support
emacs24.5emacs/24.5None applicationunknown
emboss6.5.7emboss/6.5None applicationcomputational biologyEMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
eqtlbma1.3eqtlbma/1.3None applicationbiologyPackage to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.
erne2.1.1erne/2.1None applicationcomputational biologyERNE is a short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.
esmf5.2.0rp3esmf/5.2compiler/intel/13 libraryruntime support
espresso5.0espresso/5.0compiler/intel/13:openmpi/1.8 libraryruntime support
exomiser7.2exomiser/7.2None applicationcomputational biologyThe Exomiser is a Java program that finds potential disease-causing variants from whole-exome or whole-genome sequencing data.
exonerate2.2exonerate/2.2None applicationcomputational biologyExonerate - a generic tool for sequence alignment.
express1.5express/1.5None applicationlife sciencesexpress - Streaming quantification for high-throughput sequencing
fastqc0.10fastqc/0.10None applicationcomputational biologyfastqc - A Quality Control application for FastQ files
fastqc0.11.5fastqc/0.11None applicationcomputational biologyfastqc - A Quality Control application for FastQ files
fastx_toolkit0.0.14fastx_toolkit/0.0.14None applicationcomputational biologyFASTX Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
fftw22.1fftw2/2.1compiler/gcc/4.8 compiler/intel/13 libraryruntime support
fftw33.3fftw3/3.3compiler/gcc/4.8 compiler/gcc/4.8:openmpi/1.8 compiler/gcc/4.9 compiler/gcc/6.1:openmpi/2.0 compiler/intel/12 compiler/intel/12:openmpi/1.8 compiler/intel/13 compiler/intel/13:openmpi/1.8 compiler/intel/15 libraryruntime support
flash1.2.11flash/1.2compiler/gcc/4.9 applicationcomputational biologyFLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data.
gamess20141205R1gamess/20141205R1compiler/intel/13:openmpi/1.8 libraryruntime support
gatk3.4-46gatk/3.4None applicationcomputational biologyThe Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing 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.
gatk3.7gatk/3.7None applicationcomputational biologyThe Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyze high-throughput sequencing 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.
gaussian/0909 RevDgaussian/09/RevDNone applicationChemistry
gaussian/0909 RevEgaussian/09/RevENone applicationChemistry
gaussian/1616 RevEgaussian/16/RevANone applicationChemistry
gdal1.11gdal/1.11compiler/gcc/4.9 libraryruntime support
gdcclient1.2.0gdcclient/1.2compiler/gcc/4.9 libraryruntime support
gem2.7gem/2.7None applicationcomputational biologyGEM: High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data.
genemark-es2.3fgenemark-es/2.3fNone applicationcomputational biologyGeneMark-ES.
genemarks2.5pgenemarks/2.5pNone applicationcomputational biologyGeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
genemarks4.3genemarks/4.3None applicationcomputational biologyGeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions
geos3.5geos/3.5compiler/gcc/4.9 libraryruntime support
gflags2.1gflags/2.1None libraryunknownOnline documentation available at: https://gflags.github.io/gflags/
ghostscript9.20ghostscript/9.20None libraryruntime support
git2.7git/2.7None librarytoolsFast Version Control System
globus-cli1.2.0globus-cli/1.2None applicationtoolCommand line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases.
glog0.3.3glog/0.3None applicationUtility
glpk4.61glpk/4.61None applicationmathematicsThe GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library.
gmap2015.12.31gmap/2015.12.31None applicationcomputational biologyGMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap2017.05.08gmap/2017.05.08None applicationcomputational biologyGMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gnuplot4.6gnuplot/4.6None applicationunknownGnuplot is a portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.
grib-api1.12.3grib-api/1.12compiler/intel/13 libraryruntime support
grib-api1.14.5grib-api/1.14compiler/intel/15 compiler/pgi/14 compiler/pgi/15 libraryruntime support
gromacs4.6gromacs/4.6compiler/gcc/4.8:openmpi/1.6 libraryruntime support
gromacs5.1.4gromacs/5.1compiler/gcc/4.9:openmpi/2.0 applicationcomputational biologyGROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.
GSL1.16GSL/1.16compiler/gcc/4.9 compiler/intel/13 libraryruntime support
gtool0.7.5gtool/0.7compiler/gcc/6.1 applicationcomputational biologyGTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE.
hapflk1.3.0hapflk/1.3None applicationpackagehapflk is a software implementing the hapFLK [1] and FLK [2] tests for the detection of selection signatures based on multiple population genotyping data.
harminv1.4harminv/1.4compiler/gcc/4.9 libraryruntime support
hdf44.2hdf4/4.2compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
hdf51.8hdf5/1.8compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 None libraryruntime support
hdf51.8.15hdf5/1.8compiler/intel/15 compiler/intel/16 libraryruntime support
hiddendomains2.3hiddendomains/2.3None applicationchip-seqhiddenDomains is a suite of programs used to identify significant enrichment of ChIP-seq reads that span large domains.
hisat22.0.5hisat2/2.0None applicationcomputational biologyHISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) to a population of human genomes (as well as to a single reference genome).
hmmer3.1hmmer/3.1compiler/gcc/4.8:openmpi/1.6 compiler/gcc/4.8:openmpi/1.8 applicationcomputational biologyHMMER biosequence analysis using profile hidden Markov models
htseq0.5.4p5htseq/0.5.4p5None applicationcomputational biologyHTSeq - Analysing high-throughput sequencing data with Python
htseq0.6.1p1htseq/0.6.1p1None applicationcomputational biologyHTSeq - Analysing high-throughput sequencing data with Python
htslib1.3.2htslib/1.3None applicationcomputational biologyHTSlib is an implementation of a unified C library for accessing common file formats.
HTSlib1.2HTSlib/1.2compiler/gcc/4.8 applicationcomputational biologyHTSlib - the core library used by samtools and bcftools.
humann20.9.9humann2/0.9None applicationcomputational biologyHUMAnN2 is the next generation of HUMAnN (HMP Unified Metabolic Analysis Network).
idba1.1.3idba/1.1None applicationcomputational biologyIDBA is a practical iterative De Bruijn Graph De Novo Assembler for sequence assembly in bioinfomatics.
idr2.0idr/2.0None applicationcomputational biologyThe 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.
igraph0.7igraph/0.7compiler/gcc/4.9 libraryruntime support
impute22.3.2impute2/2.3None applicationcomputational biologyIMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes.
intel-mkl12intel-mkl/12None librarytoolsNumerical library, contains blas/lapack
intel-mkl13intel-mkl/13None librarytoolsNumerical library, contains blas/lapack
intel-mkl15intel-mkl/15None librarytoolsNumerical library, contains blas/lapack
intel-mkl16intel-mkl/16None librarytoolsNumerical library, contains blas/lapack
interproscan5.23-62.0interproscan/5.23compiler/gcc/4.8 applicationcomputational biologyScans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan5.24-63.0interproscan/5.24compiler/gcc/4.8 applicationcomputational biologyScans a range of protein signatures against your sequences and provides protein functional analysis.
interproscan5.8-49.0interproscan/5.8None applicationcomputational biologyScans a range of protein signatures against your sequences and provides protein functional analysis.
irods4.1irods/4.1None applicationunknownThe integrated Rule-Oriented Data System (iRODS) is open source data management software used by research organizations and government agencies worldwide. This module includes the icommands client programs only.
jags3.4jags/3.4compiler/intel/15 applicationmathematicsJAGS is Just Another Gibbs Sampler.
jags4.2jags/4.2compiler/gcc/4.9 compiler/intel/15 applicationmathematicsJAGS is Just Another Gibbs Sampler.
jamm1.0.7r2jamm/1.0.7r2None applicationcomputational biologyJAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately.
java1.6java/1.6None applicationsystemJava JDK.
java1.7java/1.7None applicationsystemJava JDK.
java1.8java/1.8None applicationsystemJava JDK.
jellyfish2.2.0jellyfish/2.2None applicationcomputational biologyJellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
jmosaics1.10jmosaics/1.10None applicationcomputational biologyJoint analysis of multiple ChIP-Seq data sets.
kaiju1.4.4kaiju/1.4compiler/gcc/4.9 libraryruntime support
kaiju1.5.0kaiju/1.5compiler/gcc/4.9 applicationBioinformatics
kalign2.03kalign/2.03None applicationcomputational biologyKalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
kallisto0.42.3kallisto/0.42compiler/gcc/4.8 libraryruntime support
khmer2.0khmer/2.0None applicationcomputational biologyKhmer is tools for in-memory nucleotide sequence k-mer counting, filtering, graph traversal and more.
lammps10Aug2015lammps/10Aug2015compiler/intel/15:openmpi/1.8 libraryruntime support
lammps10Feb2017lammps/10Feb2017compiler/gcc/6.1:openmpi/2.0 compiler/intel/15:openmpi/1.10 libraryruntime support
lammps15MAY2015lammps/15May15compiler/gcc/4.9:openmpi/1.8 compiler/gcc/4.9:openmpi/2.1 libraryruntime support
lammps30Oct2014lammps/30Oct2014compiler/gcc/4.8:openmpi/1.8 libraryruntime support
lammps31Jan2014lammps/31Jan2014compiler/gcc/4.8:openmpi/1.6 libraryruntime support
last1.0last/1.0compiler/gcc/4.9 libraryruntime support
libctl3.2libctl/3.2compiler/gcc/4.9 compiler/gcc/6.1 libraryruntime support
libint1.1libint/1.1compiler/gcc/4.7 applicationComputational ChemistryLibint is a software stack for computing integrals used in molecular quantum mechanics
libxc2.2.3libxc/2.2compiler/intel/13 libraryruntime support
libxml22.7libxml2/2.7compiler/gcc/4.9 libraryruntime support
libxml22.9libxml2/2.9compiler/gcc/4.9 libraryruntime support
libxslt1.1libxslt/1.1compiler/gcc/4.9 libraryruntime support
LIS7.0rLIS/7.0rcompiler/intel/13:openmpi/1.8 libraryruntime support
lmdb0.9lmdb/0.9None libraryunknownLightning memory-mapped database library.
lmodlmodlmod/lmodNone applicationunknownLmod: An Environment Module System
lsdyna5.1.1lsdyna/5.1.1None applicationunknown
lsdyna6.0.0lsdyna/6.0.0None applicationunknown
lsdyna6.1.2lsdyna/6.1.2None applicationunknown
lsdyna7.0.0lsdyna/7.0.0None applicationunknown
lsdyna7.1.1lsdyna/7.1.1None applicationunknown
lsdyna8.0.0lsdyna/8.0.0None applicationunknown
lsdyna8.0.1lsdyna/8.0.1None applicationunknown
lsdyna8.1.0lsdyna/8.1.0None applicationunknown
lsdyna9.0.1lsdyna/9.0.1None applicationunknown
lynx2.8.8lynx/2.8None applicationtoolLynx is a text browser for the World Wide Web.
m41.4m4/1.4None applicationUtilitiesGNU M4 is an implementation of the traditional Unix macro processor.
macs22.1.0macs2/2.1None applicationcomputational biologyMACS -- Model-based Analysis of ChIP-Seq
mafft7.149mafft/7.149None applicationbiologyMultiple alignment program for amino acid or nucleotide sequences
mapsplice2.2.0mapsplice/2.2None applicationcomputational biologyMapSplice 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.
maq0.7maq/0.7None applicationcomputational biologymaq - Mapping and Assembly with Quality.
mathematica10.4mathematica/10.4None applicationunknown
mathematica11.0mathematica/11.0None applicationunknown
mathematica9.0mathematica/9.0None applicationunknown
matio1.5matio/1.5compiler/gcc/4.9 libraryruntime support
matlabr2012bmatlab/r2012bNone applicationunknown
matlabr2013bmatlab/r2013bNone applicationunknown
matlabr2014bmatlab/r2014bNone applicationunknown
matlabr2015bmatlab/r2015bNone applicationunknown
matlabr2016amatlab/r2016aNone applicationunknown
matlabr2016bmatlab/r2016bNone applicationunknown
matlabr2017amatlab/r2017aNone applicationunknown
mauve2.4mauve/2.4None applicationcomputational biologymauve - Multiple Genome Alignment.
maven3.2maven/3.2None applicationsystemApache Maven is a software project management and comprehension tool.
maven3.5maven/3.5None applicationsystemApache Maven is a software project management and comprehension tool.
mcl14.137mcl/14.137None applicationcomputational biologyMCL
meep1.3meep/1.3None libraryruntime support
meep_parallel1.3meep_parallel/1.3compiler/gcc/4.9:openmpi/1.10 libraryruntime support
meerkat0.189meerkat/0.1None applicationcomputational biologyMeerkat is designed to identify structural variations
megahit1.1megahit/1.1None applicationcomputational biologyMEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
megahit-gpu1.1megahit-gpu/1.1None applicationcomputational biologyMEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph.
MEME4.11.3MEME/4.11None applicationcomputational biologyThe MEME suite is a collection of tools for the discovery and analysis of sequence motifs. It is hosted at http://meme-suite.org/.
meme-suite4.12.0meme-suite/4.12compiler/gcc/6.1:openmpi/2.0 applicationcomputational biology
MET5.0MET/5.0None libraryruntime support
metaphlan1.7metaphlan/1.7None applicationcomputational biologyMetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan2.6.0metaphlan/2.6None applicationmetagenomic phylogenetic analysisMetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metasv0.5.4metasv/0.5None applicationcomputational biologyAn accurate and integrative structural-variant caller for next generation sequencing.
metavelvet1.2.01metavelvet/1.2None applicationcomputational biologyMetaVelvet is an extension of Velvet assembler to de novo metagenome assembly from short sequence reads.
miRDeep2.0.0miRDeep/2.0None applicationcomputational biologymiRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs.
mongodb-client3.2mongodb-client/3.2None applicationUtilityClient programs for MongoDB.
mongodb-client3.4mongodb-client/3.4None applicationUtilityClient programs for MongoDB.
mono4.6mono/4.6None applicationcompilerMono is an open source implementation of Microsoft's .NET Framework based on the ECMA standards for C# and the Common Language Runtime.
moose1.0moose/1.0compiler/gcc/6.1:openmpi/2.0 libraryruntime support
mosaik2.2mosaik/2.2None applicationcomputational biologyMOSAIK is a reference-guided aligner for next-generation sequencing technologies.
mothur1.35.1mothur/1.35compiler/gcc/4.9:openmpi/1.10 libraryruntime support
mpb1.5mpb/1.5compiler/gcc/6.1:openmpi/2.0 libraryruntime support
mpiblast1.6mpiblast/1.6compiler/gcc/4.8:openmpi/1.6 applicationcomputational biologympiBLAST is a freely available, open-source, parallel implementation of NCBI BLAST.
mpich21.5mpich2/1.5compiler/gcc/4.7 libraryruntime support
mplus6.12mplus/6.12None applicationunknownMplus is a latent variable modeling program with a wide variety of analysis capabilities.
mplus7.0mplus/7.0None applicationunknownMplus is a latent variable modeling program with a wide variety of analysis capabilities.
mugsyv1r2.3mugsy/v1r2.3None applicationcomputational biology
multiqc0.8multiqc/0.8None applicationcomputational biologyAggregate results from bioinformatics analyses across many samples into a single report
multiwell2017multiwell/2017compiler/gcc/6.1:openmpi/2.1 applicationchemistryMultiWell calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems that consist of stable species and multiple isomerization and/or dissociation reactions.
mummer3.23mummer/3.23None applicationcomputational biologyMUMmer - A modular system for the rapid whole genome alignment of finished or draft sequence
muscle3.8muscle/3.8None applicationcomputational biologyPopular multiple alignment software
music1.0music/1.0None applicationcomputational biologyMUSIC is an algorithm for identification of enriched regions at multiple scales in the read depth signals from ChIP-Seq experiments.
mutect1.1mutect/1.1None applicationcomputational biologyMuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes.
mvapich21.9mvapich2/1.9compiler/intel/13 libraryruntime support
mxnet0.9.3amxnet/0.9.3None applicationAIMXNet is an open-source deep learning framework that allows you to define, train, and deploy deep neural networks on a wide array of devices, from cloud infrastructure to mobile devices.
mytaxa1.0mytaxa/1.0None applicationcomputational biologyMyTaxa - Assign taxonomy to metagenomic fragments.
NCL6.0NCL/6.0compiler/intel/13 applicationutilityA library of graphics utilites from the Natl. Center for Atmospheric Research.
NCL6.1NCL/6.1None applicationutilityA library of graphics utilites from the Natl. Center for Atmospheric Research.
NCL6.3NCL/6.3None applicationutilityA library of graphics utilites from the Natl. Center for Atmospheric Research.
NCL6.4NCL/6.4None applicationutilityA library of graphics utilites from the Natl. Center for Atmospheric Research.
NCO4.3NCO/4.3compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 libraryruntime support
NCO4.4NCO/4.4compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 libraryruntime support
NCO4.4.6NCO/4.4compiler/intel/15 compiler/intel/16 compiler/pgi/15 libraryruntime support
NCO4.5.5NCO/4.5compiler/intel/15 libraryruntime support
NCO4.6.6NCO/4.6compiler/intel/15 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
netcdf4.1netcdf/4.1compiler/intel/13 libraryruntime support
netcdf4.2netcdf/4.2compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
netcdf4.3netcdf/4.3compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
netcdf4.4netcdf/4.4compiler/gcc/4.9 libraryruntime support
netcdf4.4.0netcdf/4.4compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
netsurfp1.0cnetsurfp/1.0None applicationcomputational biologyNetSurfP predicts the surface accessibility and secondary structure of amino acids in an amino acid sequence. The method also simultaneously predicts the reliability for each prediction, in the form of a Z-score. The Z-score is related to the surface prediction, and not the secondary structure.
NUWRFNUWRFNUWRF/intelNone libraryruntime support
nwchem6.3nwchem/6.3compiler/intel/13:openmpi/1.6 libraryruntime support
nwchem6.5nwchem/6.5compiler/intel/13:openmpi/1.8 libraryruntime support
nwchem6.6nwchem/6.6compiler/intel/13:openmpi/1.8 libraryruntime support
oases0.2.09oases/0.2compiler/gcc/6.1 applicationcomputational biologyOases is de novo transcriptome assembler based on the Velvet genome assembler core.
octave4.2octave/4.2None applicationengineeringGNU Octave is a high-level language, primarily intended for numerical computations. It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab.
openbugs3.2openbugs/3.2None applicationstatisticsBUGS is a software package for performing Bayesian inference Using Gibbs Sampling.
opencl1.2opencl/1.2None libraryunknownThis runtime software package adds OpenCL CPU device support on systems with Intel Core and Intel Xeon processors.
opencv2.4.11opencv/2.4None libraryunknownIf the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself.
opencv3.1.0opencv/3.1None libraryunknownIf the library finds Intel's Integrated Performance Primitives on the system, it will use these proprietary optimized routines to accelerate itself.
openmpi1.10.2openmpi/1.10compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
openmpi1.6openmpi/1.6compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
openmpi1.8openmpi/1.8compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
openmpi2.0openmpi/2.0compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
openmpi2.0.1openmpi/2.0compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 libraryruntime support
openmpi2.1openmpi/2.1compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
openmpi2.1.1openmpi/2.1compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/gcc/5.4 compiler/gcc/6.1 libraryruntime support
openmx3.7openmx/3.7compiler/intel/13:openmpi/1.8 libraryruntime support
orthofinder1.1.8orthofinder/1.1None applicationcomputational biologyOrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
p7zip16.02p7zip/16.02None applicationcompressionp7zip is a port of 7za.exe for POSIX systems.
pandaseq2.9pandaseq/2.9compiler/gcc/4.9 applicationbioinforomaticsPANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
parsinsert1.04parsinsert/1.04None applicationcomputational biologyParsInsert efficiently produces both a phylogenetic tree and taxonomic classification for sequences for microbial community sequence analysis. This is a C++ implementation of the Parsimonious Insertion algorithm
pbh5tools0.8.0pbh5tools/0.8None applicationcomputational biologypbh5tools -- tools for manipulating HDF5 files produced by Pacific Biosciences. Specifically, this package provides functionality for manipulating and extracting data from "cmp.h5" and "bas.h5" files.
peakranger1.18peakranger/1.18None applicationcomputational biologyPeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data.
peakzilla1.0peakzilla/1.0None applicationcomputational biologyPeakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at hight accuracy and resolution.
pepr1.1.18pepr/1.1None applicationcomputational biologyPeak-calling and Prioritization pipeline for replicated ChIP-Seq data.
peridigm1.5peridigm/1.5compiler/gcc/4.9:openmpi/1.10 libraryruntime support
perl5.22perl/5.22None applicationperlThe Perl Programming Language
perl-mongodb1.2.2perl-mongodb/1.2None applicationUtilityThis is the official Perl driver for MongoDB.
pesmf5.2.0rp3pesmf/5.2compiler/intel/13:openmpi/1.6 libraryruntime support
petsc3.6petsc/3.6compiler/gcc/6.1:openmpi/2.0 libraryruntime support
phdf51.8phdf5/1.8compiler/gcc/4.8:openmpi/1.6 libraryruntime support
phdf51.8.15phdf5/1.8compiler/gcc/4.7:openmpi/1.8 compiler/gcc/4.8:openmpi/1.8 compiler/gcc/4.9:openmpi/1.10 compiler/intel/15:openmpi/1.10 compiler/pgi/12:openmpi/1.8 compiler/pgi/13:openmpi/1.8 compiler/pgi/14:openmpi/1.8 compiler/pgi/15:openmpi/1.8 libraryruntime support
phobius1.01phobius/1.01None applicationcomputational biologyPhobius is a combined transmembrane topology and signal peptide predictor.
phonopy1.11.12phonopy/1.11None libraryruntime support
phrap0.990329phrap/0.9compiler/gcc/4.8 applicationcomputational biologyPhrap is a program for assembling shotgun DNA sequence data. Cross_match is a general purpose utility for comparing any two DNA sequence sets using a 'banded' version of swat. Swat is a program for searching one or more DNA or protein query sequences, or a query profile, against a sequence database, using an efficient implementation of the Smith-Waterman or Needleman-Wunsch algorithms with linear (affine) gap penalties.
phylip3.696phylip/3.696compiler/gcc/4.9 applicationcomputational biologyPHYLIP (the PHYLogeny Inference Package) is a package of programs for inferring phylogenies (evolutionary trees).
picard1.139picard/1.1None applicationcomputational biologyA set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard2.9.0picard/2.9None applicationcomputational biologyA set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picrust1.1.0picrust/1.1None applicationmetagenomicThe PICRUSt project aims to support prediction of the unobserved character states in a community of organisms from phylogenetic information about the organisms in that community.
pindel0.2.5b8pindel/0.2None applicationcomputational biology
plink1.90plink/1.90None applicationcomputational biologyPLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
plinkseq0.10plinkseq/0.10None applicationcomputational biologyPLINK/SEQ is an open-source C/C++ library for working with human genetic variation data.
pnetcdf4.2pnetcdf/4.2compiler/gcc/4.8:openmpi/1.6 libraryruntime support
pnetcdf4.4pnetcdf/4.4compiler/gcc/4.9:openmpi/1.10 libraryruntime support
PNG1.2.50PNG/1.2compiler/intel/13 libraryruntime support
pplacer1.1pplacer/1.1None applicationcomputational biologyPplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment.
primer32.3.7primer3/2.3None applicationcomputational biologyPrimer3 picks primers for PCR reactions
prinseq-lite0.20.4prinseq-lite/0.20None applicationcomputational biologyPRINSEQ can be used to filter, reformat, or trim your genomic and metagenomic sequence data.
prodigal2.60prodigal/2.60None applicationcomputational biologyProdigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
proj4.9proj/4.9compiler/gcc/4.9 libraryruntime support
prokka1.12prokka/1.12None applicationbioinformaticsProkka is a software tool for the rapid annotation of prokaryotic genomes.
pyclone0.13pyclone/0.13None applicationcomputational biologyPyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples.
pyfasta0.5pyfasta/0.5None applicationcomputational biologyPyfasta - fast, memory-efficient, pythonic (and command-line) access to fasta sequence files.
pymeteo0.5pymeteo/0.5None applicationgeoscienceGeneral meteorological routines, skew-T/log-p plotting and working with CM1 model data.
pymongo3.0.3pymongo/3.0None applicationUtilityPyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pymongo3.3.0pymongo/3.3None applicationUtilityPyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
python2.7python/2.7None applicationsystem
python3.3python/3.3None applicationsystem
python3.4python/3.4None applicationsystem
python3.5python/3.5None applicationsystem
python3.6python/3.6None applicationsystem
python-openstackclient2.1.0python-openstackclient/2.1None applicationUtilityOpenStackClient (aka OSC) is a command-line client for OpenStack that brings the command set for Compute, Identity, Image, Object Store and Block Storage APIs together in a single shell with a uniform command structure.
qctool1.4qctool/1.4None applicationcomputational biologyQCTOOL is a command-line utility program for basic quality control of gwas datasets.
qiime1.8qiime/1.8None applicationcomputational biologyQIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).
qiime1.9qiime/1.9None applicationcomputational biologyQIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).
quast4.1quast/4.1None applicationcomputational biologyQUAST. the QUality ASsessment Tool for genome assemblies.
quast4.4quast/4.4None applicationcomputational biologyQUAST evaluates genome assemblies by computing various metrics.
quast4.5quast/4.5None applicationcomputational biologyQUAST evaluates genome assemblies by computing various metrics.
R3.0R/3.0compiler/intel/12 compiler/intel/13 None libraryruntime support
R3.1R/3.1None libraryruntime support
R3.2R/3.2compiler/intel/15 None libraryruntime support
R3.3R/3.3None libraryruntime support
R3.4R/3.4None applicationmathematics
RAPSearch22.19RAPSearch2/2.19None applicationcomputational biologyRAPSearch2 is a tool for fast protein similarity searches.
ray2.3ray/2.3compiler/gcc/4.8:openmpi/1.6 compiler/gcc/4.8:openmpi/1.8 applicationcomputational biologyRay -- Parallel genome assemblies for parallel DNA sequencing.
repeatmasker4.0repeatmasker/4.0None applicationcomputational biologyRepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
rmblast2.28rmblast/2.28compiler/gcc/4.8 applicationcomputational biologyRMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler.
rnammer1.2rnammer/1.2None applicationcomputational biologyRNAmmer predicts 5s/8s, 16s/18s, and 23s/28s ribosomal RNA in full genome sequences.
root6.06.00root/6.06compiler/gcc/4.9 applicationbig dataIt provides all the functionalities needed to deal with big data processing, statistical analysis, visualisation and storage.
rosetta3.8rosetta/3.8compiler/gcc/4.9:openmpi/2.0 applicationcomputational biologyThe Rosetta software suite includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
r-regresshaplo1.0r-regresshaplo/1.0None applicationbiologyThis package reconstructs haplotypes from a BAM file using a penalized regression approach.
rsem1.2rsem/1.2None applicationcomputational biologyRSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
rsem1.3rsem/1.3None applicationcomputational biologyRSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
r-seqminer6.0r-seqminer/6.0None applicationbiologySEQMINER is for sequencing variant annotation, data integration and query in R.
ruby2.1ruby/2.1None applicationsystem
r-vcfr1.5.0r-vcfr/1.5None applicationbiologyA package to manipulate and visualize VCF data in R.
saga2.1saga/2.1compiler/gcc/4.9 applicationGISSAGA: System for Automated Geoscientific Analyses.
saga2.2saga/2.2compiler/gcc/4.9 applicationGISSAGA: System for Automated Geoscientific Analyses.
saga2.3saga/2.3compiler/gcc/4.9 applicationGISSAGA: System for Automated Geoscientific Analyses.
sage6.3sage/6.3None applicationmathematics'Sage is a free open-source mathematics software system licensed under the GPL. It builds on top of many existing open-source packages: NumPy, SciPy, matplotlib, Sympy, Maxima, GAP, FLINT, R and many more.' Mission: 'Creating a viable free open source alternative to Magma, Maple, Mathematica and Matlab.'
salmon0.6.0salmon/0.6None applicationcomputational biologyHighly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon0.8.0salmon/0.8None applicationcomputational biologyHighly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
samtools0.1samtools/0.1None applicationcomputational biologySAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
samtools1.1samtools/1.1compiler/gcc/4.8 applicationcomputational biologySAM Tools - a generic tool for the sam format alignments.
samtools1.2samtools/1.2compiler/gcc/4.8 applicationcomputational biologySAM Tools - a generic tool for the sam format alignments.
samtools1.3.1samtools/1.3None applicationcomputational biologySAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
sas9.3sas/9.3None applicationApplicationsSAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.
sas9.4sas/9.4None applicationApplicationsSAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.
scan-for-matches1.0scan-for-matches/1.0None applicationcomputational biologyscan_for_matches is a utility written in C for locating patterns in DNA or protein FASTA files.
scip4.0.0scip/4.0None applicationconstraint integer programmingSCIP is currently one of the fastest non-commercial solvers for mixed integer programming (MIP) and mixed integer nonlinear programming (MINLP).
scons2.5scons/2.5None applicationutilitySCons: A software construction tool.
seedme1.2seedme/1.2None applicationUtilityClient program for SeedMe.org.
seqtk1.2seqtk/1.2None applicationcomputational biologySeqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
settargsettargsettarg/settargNone applicationunknown
sff2fastq0.9sff2fastq/0.9None applicationcomputational biologysff2fast extracts 454 Genome Sequencer reads from a SFF file and converts them into a FASTQ formatted output
shapeit2.0shapeit/2.0None applicationcomputational biologySHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
shengbte1.1.1shengbte/1.1compiler/gcc/4.9:openmpi/1.10 libraryruntime support
shrimp2.2shrimp/2.2None applicationcomputational biologySHRiMP is a software package for aligning genomic reads against a target genome.
shtns2.8shtns/2.6compiler/intel/15 applicationmath
sickle1.2sickle/1.210None applicationcomputational biologyA windowed adaptive trimming tool for FASTQ files using quality
siesta4.1.3siesta/4.1compiler/gcc/4.9:openmpi/1.10 compiler/intel/13:openmpi/1.8 libraryruntime support
signalp4.1signalp/4.1None applicationcomputational biologysignalp predicts the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms: Gram-positive bacteria, Gram-negative bacteria, and eukaryotes.
simrna3.20simrna/3.20None applicationcomputational biologySimRNA is a tool for simulations of RNA conformational dynamics
singularity2.2singularity/2.2None applicationsystemApplication containers enabling mobility of compute.
singularity2.3singularity/2.3None applicationsystemApplication containers enabling mobility of compute.
snap2013-11-29snap/2013-11-29None applicationcomputational biologySNAP - (Semi-HMM-based Nucleic Acid Parser) gene prediction tool.
snp-pipeline0.6snp-pipeline/0.6None applicationcomputational biologySNP Pipeline is a pipeline for the production of SNP matrices from sequence data used in the phylogenetic analysis of pathogenic organisms sequenced from samples of interest to food safety.
snptest2.5.2snptest/2.5None applicationcomputational biologySNPTEST is a program for the analysis of single SNP association in genome-wide studies.
soapdenovo2r240soapdenovo2/r240None applicationcomputational biologysoapdenovo2 - novel short-read assembly method that can build a de novo draft assembly for the human-sized genomes
soapdenovo-trans1.04soapdenovo-trans/1.04None applicationcomputational biologySOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
spades3.10.1spades/3.10None applicationcomputational biologySPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades3.11.0spades/3.11None applicationcomputational biologySPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades3.8.2spades/3.8None applicationcomputational biologySPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spglib1.9.9spglib/1.9compiler/gcc/4.9 libraryruntime support
spider2.0spider/2.0None applicationcomputational biologySequence-based Prediction of Local and Nonlocal Structural Features for Proteins.
spp1.11spp/1.11None applicationcomputational biologyChIP-seq peak caller
spp1.13spp/1.13None applicationcomputational biologyChIP-seq peak caller
SRAtoolkit2.8SRAtoolkit/2.8None applicationcomputational biologySRA Toolkit
star2.5.3astar/2.5compiler/gcc/4.9 applicationbiologySpliced Transcripts Alignment to a Reference
starccm10.01.010starccm/10.06None libraryruntime support
starccm9.01.011starccm/9.06None libraryruntime support
StringTie1.3.0StringTie/1.3None applicationcomputational biologyStringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts.
structure2.3structure/2.3None applicationcomputational biologyThe program structure is a free software package for using multi-locus genotype data to investigate population structure.
subread1.4subread/1.4None applicationcomputational biologyThe Subread package is developed in The Walter and Eliza Hall Institute of Medical Research, Melbourne, Australia. It consists of a suite of programs for processing next-gen sequencing data.
szip2.1szip/2.1compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 None libraryruntime support
tabix0.2tabix/0.2None applicationcomputational biologyTabix indexes a TAB-delimited genome position file in.tab.bgz and creates an index file
tagcleaner0.16tagcleaner/0.16None applicationcomputational biologyThe TagCleaner tool can be used to automatically detect and efficiently remove tag sequences (e.g. WTA tags) from genomic and metagenomic datasets. It is easily configurable and provides a user-friendly interface.
tassel3.0tassel/3.0None applicationcomputational biologyWhile 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 genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization.
tassel4.0tassel/4.0None applicationcomputational biologyWhile 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 genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization.
tassel5.1tassel/5.1None applicationcomputational biologyWhile 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 genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization.
tassel5.2tassel/5.2None applicationcomputational biologyWhile 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 genotypes1. As indicated by its title – Trait Analysis by aSSociation, Evolution and Linkage – TASSEL has multiple functions, including association study, evaluating evolutionary relationships, analysis of linkage disequilibrium, principal component analysis, cluster analysis, missing data imputation and data visualization.
tax2tree1.0tax2tree/1.0None applicationcomputational biologytax2tree - Tools for decorating taxonomy information on to a phylogenetic tree.
taxypro1.0taxypro/1.0None applicationmixture modeling for taxonomic analysis of metagenomes
taxytoolbox1.0taxytoolbox/1.0None applicationmixture modeling for taxonomic analysis of metagenomes
tensorflow0.12.1tensorflow/0.12None applicationmachine learningTensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow1.0.0tensorflow/1.0None applicationmachine learningTensorFlow is an open source software library for numerical computation using data flow graphs.
theano0.9.0theano/py27/0.9None None applicationmathematicsTheano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
tmhmm2.0ctmhmm/2.0cNone applicationcomputational biologyTMHMM 2.0 predicts transmembrane helices in proteins.
tophat2.0tophat/2.0None applicationcomputational biologyTopHat2 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.
tophat2.1.0tophat/2.1None applicationcomputational biologyTopHat2 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.
transdecoder2.0.1transdecoder/2.0None applicationcomputational biologyTransDecoder 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.
transdecoder3.0.1transdecoder/3.0None applicationcomputational biologyTransDecoder 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.
transrate0.1transrate/0.1None applicationlife sciencestransrate - Quality assessment and comparison of transcriptome assemblies
treemix1.12treemix/1.12None applicationcomputational biologyTreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
treemix1.13treemix/1.13None applicationcomputational biologyTreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
trf4.07btrf/4.0None applicationcomputational biologyTandem Repeats Finder is a program to locate and display tandem repeats in DNA sequences.
trilinos12.6trilinos/12.6compiler/gcc/4.9:openmpi/1.10 libraryruntime support
trim_galore0.4.0trim_galore/0.4None applicationcomputational biologyTrim sequences
trimmomatic0.33trimmomatic/0.33None applicationcomputational biologyTrimmomatic: A flexible read trimming tool for Illumina NGS data.
trimmomatic0.36trimmomatic/0.36None applicationcomputational biologyTrimmomatic: A flexible read trimming tool for Illumina NGS data.
trinity2.0trinity/2.0compiler/gcc/4.8 applicationcomputational biologyPackage for RNA-Seq de novo Assembly
trinity2.1trinity/2.1compiler/gcc/4.8 applicationcomputational biologyPackage for RNA-Seq de novo Assembly
trinity2.4.0trinity/2.4None applicationcomputational biologyTrinity assembles transcript sequences from Illumina RNA-Seq data.
trinityr2013-11-10trinity/r2013-11-10None applicationcomputational biologyPackage for RNA-Seq de novo Assembly
trinityr2014-04-13p1trinity/r2014-04-13p1None applicationcomputational biologyPackage for RNA-Seq de novo Assembly
trinotate2.0.2trinotate/2.0None applicationcomputational biologyTrinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
trinotater2013-11-10trinotate/r2013-11-10None applicationcomputational biologyTrinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms.
udunits22.1udunits2/2.1compiler/gcc/4.7 compiler/gcc/4.8 compiler/intel/12 compiler/intel/13 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
udunits22.2udunits2/2.2compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 libraryruntime support
upcr2.20upcr/2.20compiler/gcc/4.9:openmpi/1.8 applicationcompiler
upcr2.24upcr/2.24compiler/gcc/5.4:openmpi/2.0 applicationcompiler
usearch5.2usearch/5.2None applicationcomputational biologyUSEARCH 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.
usearch6.1usearch/6.1None applicationcomputational biologyUSEARCH 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.
usearch7.0usearch/7.0None applicationcomputational biologyUSEARCH 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.
varscan2.3varscan/2.3None applicationcomputational biologyVarScan is a platform-independent mutation caller for targeted, exome, and whole-genome resequencing data generated on Illumina, SOLiD, Life/PGM, Roche/454, and similar instruments.
vasp5.4vasp/5.4solcompiler/intel/13:openmpi/1.8 compiler/intel/15:openmpi/2.1 libraryruntime support
vasp5.4.4vasp/5.4.4compiler/intel/15:openmpi/2.1 libraryruntime support
vcftools0.1vcftools/0.1None applicationcomputational biologyVCFtools 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.
velvet1.2velvet/1.2None applicationcomputational biologyVelvet - Sequence assembler for very short reads
viennarna2.3.3viennarna/2.3None applicationcomputational biologyThe ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
wgrib22.0.6wgrib2/2.0None applicationfile processingwgrib2 is more like four drawers of kitchen utensils as well as the microwave and blender.
WRFWRFWRF/1.0compiler/intel/15:openmpi/1.10 compiler/intel/16:openmpi/1.10 compiler/pgi/15:openmpi/1.10 compiler/pgi/15:openmpi/1.10 None None None libraryruntime support
xpclr1.0xpclr/1.0None applicationcomputational biologydetecting selective sweeps via the differentiation of two populations
xzutils5.2xzutils/5.2None libraryruntime support
zerone1.0zerone/1.0None applicationcomputational biologyZerone discretizes several ChIP-seq replicates simultaneously and resolves conflicts between them. After the job is done, Zerone checks the results and tells you whether it passes the quality control.
zlib1.2zlib/1.2compiler/gcc/4.7 compiler/gcc/4.8 compiler/gcc/4.9 compiler/intel/12 compiler/intel/13 compiler/intel/15 compiler/intel/16 compiler/pgi/12 compiler/pgi/13 compiler/pgi/14 compiler/pgi/15 None libraryruntime support

 

 

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