Available Software for Rhino

HCC provides some software packages via the Singularity container software. If you do not see a desired package in the module list below, please check the Using Singularity page for the software list there.

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.

Custom GPU Anaconda Environment

If you are using custom GPU Anaconda Environment, the only module you need to load is anaconda:

module load anaconda

last generated 2019-09-15T23:19:38CDT

Name Version Module Name Prerequisites Type Domain Description
R 3.5.3 R/3.5 None application mathematics Microsoft R Open is the enhanced distribution of R from Microsoft Corporation.
abacas 1.3.1 abacas/1.3 None application computational biology ABACAS is intended to rapidly contiguate (align, order, orientate), visualize and design primers to close gaps on shotgun assembled contigs based on a reference sequence.
abayesqr 1.0 abayesqr/1.0 None application high-throughput sequencing data aBayesQR is a viral quasispecies reconstruction algorithm that employs a maximum-likelihood framework to infer individual sequences in a mixture from high-throughput sequencing data.
abricate 0.8.13 abricate/0.8 None application Biology Mass screening of contigs for antibiotic resistance genes
afni 18.2.06 afni/18.2 None application MRI AFNI is a suite of programs for looking at and analyzing 3D brain images.
afterqc 0.9.6 afterqc/0.9 None application package Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data. AfterQC 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. Currently it supports processing data from HiSeq 2000/2500/3000/4000, Nextseq 500/550, MiniSeq...and other Illumina 1.8 or newer formats.
agfusion 1.0 agfusion/1.0 None application Biology AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
agfusion 1.251 agfusion/1.251 None application Biology AGFusion is a python package for annotating gene fusions from the human or mouse genomes.
allinea 18.0 allinea/18.0 None application Utility
allinea 18.2 allinea/18.2 None application Utility
allinea 19.0 allinea/19.0 None application Utility
allinea 4.2 allinea/4.2 None application Utility
allinea 5.0 allinea/5.0 None application Utility
allinea 5.1 allinea/5.1 None application Utility
allinea 6.0 allinea/6.0 None application Utility
allinea 6.1 allinea/6.1 None application Utility
allinea 7.0 allinea/7.0 None application Utility
amos 3.1.0 amos/3.1 None application computational biology A Modular, Open-Source whole genome assembler
anaconda 2.7 anaconda/2.7 None application system
anaconda 3.3 anaconda/3.3 None application system
anaconda 3.4 anaconda/3.4 None application system
anaconda 4.3 anaconda/4.3 None application system
anaconda 4.6 anaconda/4.6 None application system
ant 1.10.1 ant/1.10 None library java Java build tool
ant 1.9.9 ant/1.9 None library java Java build tool
apkid 1.0.0 apkid/1.0 None application Malware APKiD is Android Application Identifier for Packers, Protectors, Obfuscators and Oddities - PEiD for Android.
aria2 1.23.0 aria2/1.23 None application tool aria2 is a lightweight multi-protocol & multi-source command-line download utility.
aspera-cli 3.7.7 aspera-cli/3.7 None application system IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line.
augustus 3.2.3 augustus/3.2 None application computational biology AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
augustus 3.3 augustus/3.3 None application computational biology AUGUSTUS is a gene prediction program for eukaryotes written by Mario Stanke and Oliver Keller. It can be used as an ab initio program, which means it bases its prediction purely on the sequence. AUGUSTUS may also incorporate hints on the gene structure coming from extrinsic sources such as EST, MS/MS, protein alignments and synthenic genomic alignments.
autoconf 2.69 autoconf/2.69 None application Utilities Extensible M4 macros that produce shell scripts to configure software source code packages.
autodock 4.2.6 autodock/4.2 None application Chemistry AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure.
automake 1.16.1 automake/1.16 None application Utilities Automake is a tool for automatically generating Makefile.in files compliant with the GNU Coding Standards.
awscli 1.1.120 awscli/1.11 None application utility The 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.
azcopy 7.2.0 azcopy/7.2 None application Utility AzCopy is a command-line utility designed for copying data to/from Microsoft Azure Blob and File storage, using simple commands designed for optimal performance.
bam-readcount 0.8 bam-readcount/0.8 None application computational biology The purpose of this program is to generate metrics at single nucleotide positions.
bamtools 2.3.0 bamtools/2.3 None application computational biology C++ API & command-line toolkit for working with BAM data
bamtools 2.4.1 bamtools/2.4 None application computational biology C++ API & command-line toolkit for working with BAM data
basetools/gapfiller 1.10 basetools/gapfiller/1.10 None application computational biology GapFiller is a stand-alone program for closing gaps within pre-assembled scaffolds.
basetools/sspace-standard 3.0 basetools/sspace-standard/3.0 None application computational biology SSPACE-standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data.
bbmap 37.17 bbmap/37.17 None application computational biology BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bbmap 38.06 bbmap/38.06 None application computational biology BBMap is a splice-aware global aligner for DNA and RNA sequencing reads.
bcftools 1.3.1 bcftools/1.3 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools 1.8 bcftools/1.8 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcftools 1.9 bcftools/1.9 None application computational biology BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. All commands work transparently with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands accept VCF, bgzipped VCF and BCF with filetype detected automatically even when streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed VCF and BCF and streams will work in most, but not all situations.
bcl2fastq2 2.20.0.422 bcl2fastq2/2.20 None application computational biology The Illumina bcl2fastq2 Conversion Software v2.20 demultiplexes sequencing data and converts base call (BCL) files into FASTQ files.
beagle 4.1_21Jan17.6cc beagle/4.1 None application Biology Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beagle 5.1_24Aug19.3e8 beagle/5.1 None application Biology Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection.
beast 1.10 beast/1.10 None application biology BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
beast 1.8 beast/1.8 None application biology BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC.
beast2 2.4 beast2/2.4 None application biology BEAST 2 is a cross-platform program for Bayesian phylogenetic analysis of molecular sequences.
bedops 2.4.35 bedops/2.4 None application computational biology BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale.
bedtools 2.24.0 bedtools/2.24 None application computational biology A powerful toolset for genome arithmetic
bedtools 2.27.1 bedtools/2.27 None application computational biology A powerful toolset for genome arithmetic
beta 1.0.7 beta/1.0 None application computational biology Binding and Expression Target Analysis (BETA) is a software package that integrates ChIP-seq of transcription factors or chromatin regulators with differential gene expression data to infer direct target genes.
bfc r181 bfc/r181 None application Biology BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data.
bicseq2-norm 0.2.4 bicseq2-norm/0.2 None application bioinformatics BICseq2-norm is for normalizing potential biases in the sequencing data.
bicseq2-seg 0.7.2 bicseq2-seg/0.7 None application bioinformatics BICseq2-seg is for detecting CNVs based on the normalized data given by BICseq2-norm.
binutils 2.30 binutils/2.30 None application Utilities The GNU Binutils are a collection of binary tools.
bioawk 1.0 bioawk/1.0 None application Biology BWK awk modified for biological data
bioconductor 3.4 bioconductor/3.4 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor 3.8 bioconductor/3.8 None application computational biology Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data.
bioconductor-ballgown 2.2.0 bioconductor-ballgown/2.2 None application computational biology Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.
bioconductor-jmosaics 1.10 bioconductor-jmosaics/1.10 None application computational biology Joint analysis of multiple ChIP-Seq data sets.
biodata 1.0 biodata/1.0 None application computational biology Static data resources for bioinformatics/computational biology.
biom-format 2.1 biom-format/2.1 None application computational biology The BIOM file format (canonically pronounced biome) is designed to be a general-use format for representing biological sample by observation contingency tables. BIOM is a recognized standard for the Earth Microbiome Project and is a Genomics Standards Consortium supported project.
bioperl 1.6.924 bioperl/1.6 None application computational biology BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
bioperl 1.7.2 bioperl/1.7 None application computational biology BioPerl is a collection of Perl modules that facilitate the development of Perl scripts for bioinformatics applications.
biopython 1.70 biopython/py27/1.70 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.70 biopython/py35/1.70 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.70 biopython/py36/1.70 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.71 biopython/py27/1.71 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.71 biopython/py36/1.71 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
biopython 1.71 biopython/py35/1.71 None application biological computation Biopython is a set of freely available tools for biological computation written in Python by an international team of developers.
blast 2.6.0 blast/2.6 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
blast 2.7.1 blast/2.7 None application computational biology NCBI BLAST+ sequence alignment package. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches.
boost 1.70 boost/1.70 compiler/gcc/9.1 application System Environment/Base Boost provides free peer-reviewed portable C++ source libraries.
bowtie 2.2.8 bowtie/2.2 None application computational biology Fast and sensitive read alignment
bowtie 2.3.5 bowtie/2.3 None application computational biology Fast and sensitive read alignment
braker2 2.1.2 braker2/2.1 None application computational biology BRAKER2 is an extension of BRAKER1 which allows for fully automated training of the gene prediction tools GeneMark-EX and AUGUSTUS from RNA-Seq and/or protein homology information, and that integrates the extrinsic evidence from RNA-Seq and protein homology information into the prediction.
breakdancer 1.4 breakdancer/1.4 None application computational biology BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads.
breakseq2 2.2 breakseq2/2.2 None application computational biology BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants.
bsmap 2.90 bsmap/2.90 None application Mapping BSMAP is a short reads mapping software for bisulfite sequencing reads.
busco/py27 3.0.2 busco/py27/3.0 None application computational biology BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
busco/py35 3.0.2 busco/py35/3.0 None application computational biology BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
busco/py36 3.0.2 busco/py36/3.0 None application computational biology BUSCO provides measures for quantitative assessment of genome assembly, gene set, and transcriptome completeness based on evolutionarily informed expectations of gene content from near-universal single-copy orthologs selected from OrthoDB.
bwa 0.6.2 bwa/0.6 None application computational biology Burrow-Wheeler Aligner for short-read alignment.
bwa 0.7.17 bwa/0.7 None application computational biology Burrow-Wheeler Aligner for short-read alignment.
bx-python 0.8.1 bx-python/py35/0.8 None application computational biology Tools for manipulating biological data, particularly multiple sequence alignments
bx-python 0.8.1 bx-python/py36/0.8 None application computational biology Tools for manipulating biological data, particularly multiple sequence alignments
bx-python 0.8.1 bx-python/py27/0.8 None application computational biology Tools for manipulating biological data, particularly multiple sequence alignments
canu 1.7 canu/1.7 None application computational biology Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION).
carnac-lr 1.0.0 carnac-lr/1.0 None application computational biology Clustering coefficient-based Acquisition of RNA Communities in Long Read
cas-offinder 2.4 cas-offinder/2.4 None application Biology Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
ccat 3.0 ccat/3.0 None application computational biology A software package for the analysis of ChIP-seq data with negative control.
cellranger 3.0.2 cellranger/3.0 None application computational biology Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate feature-barcode matrices and perform clustering and gene expression analysis.
clove 0.17 clove/0.17 None application computational biology CLOVE: Classification of genomic fusions into structural variation events.
clustalw 2.1 clustalw/2.1 None application computational biology ClustalW2 is a multiple sequence alignment tool for the alignment of DNA or protein sequences.
cmake 2.8.10.2 cmake/2.8 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.10.3 cmake/3.10 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.11.3 cmake/3.11 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.14.5 cmake/3.14 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.5.0 cmake/3.5 None application system CMake is an extensible, open-source system that manages the build process
cmake 3.7.1 cmake/3.7 None application system CMake is an extensible, open-source system that manages the build process
codonw 1.4.4 codonw/1.4 None application computational biology CodonW is a programme designed to simplify the Multivariate analysis (correspondence analysis) of codon and amino acid usage.
compiler/gcc 9.1 compiler/gcc/9.1 None application compiler
compiler/intel 19 compiler/intel/19 None application compiler
compiler/pgi 19 compiler/pgi/19 None application compiler
connectome-workbench 1.3.1 connectome-workbench/1.3 None application neuroimaging Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project
cutadapt 1.13 cutadapt/1.13 None application NGS data Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
cutadapt 1.4 cutadapt/1.4 None application NGS data Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
deap 1.0 deap/1.0 None application computer science DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas.
deeptools 2.5.4 deeptools/2.5 None application computational biology
defiant 2019.03.02 defiant/2019.03.02 None application computational biology Differential methylation, Easy, Fast, Identification and ANnoTation.
delly 0.8.1 delly/0.8 None application Biology Structural variant discovery by integrated paired-end and split-read analysis
detectron 2018.09.11 detectron/py27/2018.09.11 None application object detection FAIR's research platform for object detection research, implementing popular algorithms like Mask R-CNN and RetinaNet.
diamond 0.9.25 diamond/0.9 None application Computational Biology Accelerated BLAST compatible local sequence aligner
drep 2.3.2 drep/2.3 None application Biology De-replication of microbial genomes assembled from multiple samples
eigen 3.3.3 eigen/3.3 None application C++ C++ template library for linear algebra
emacs 26.2 emacs/26.2 None application Utility GNU Emacs is an extensible, customizable text editor.
ensembl-vep 96.0 ensembl-vep/96.0 None application Biology The VEP determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
entrez-direct 10.0 entrez-direct/10.0 None application Entrez Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
entrez-direct 11.0 entrez-direct/11.0 None application Entrez Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window.
eqtlbma 1.3 eqtlbma/1.3 None application biology Package to detect eQTLs jointly in multiple subgroups (e.g. tissues) via Bayesian Model Averaging.
espresso 6.4.1 espresso/6.4 compiler/intel/19:openmpi/4.0 library runtime support
ete3 3.1.1 ete3/3.1 None application NCBI Python package for building, comparing, annotating, manipulating and visualising trees. It provides a comprehensive API and a collection of command line tools, including utilities to work with the NCBI taxonomy tree.
export2graphlan 0.20 export2graphlan/0.20 None application bioinformatics export2graphlan is a conversion software tool for producing both annotation and tree file for GraPhlAn.
fargene 0.1 fargene/0.1 None application bioinformatics Fragmented Antibiotic Resistance Gene iENntifiEr takes either fragmented metagenomic data or longer sequences as input and predicts and delivers full-length antiobiotic resistance genes as output
fastqc 0.11.7 fastqc/0.11 None application computational biology fastqc - A Quality Control application for FastQ files
faststructure 1.0 faststructure/1.0 None application computational biology A variational framework for inferring population structure from SNP genotype data.
fasttree 2.1.10 fasttree/2.1 None application computational biology FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences.
fenics 2018.1.0 fenics/2018.1 None application partial differential equations FEniCS is a collection of free software for automated, efficient solution of differential equations
fftw3 3.3 fftw3/3.3 compiler/intel/19:openmpi/4.0 library runtime support
fgbio 0.8.0 fgbio/0.8 None application Genomics A set of tools for working with genomic and high throughput sequencing data, including UMIs
figtree 1.4.4 figtree/1.4 None application Utilities FigTree is designed as a graphical viewer of phylogenetic trees and as a program for producing publication-ready figures.
fqtrim 0.9.7 fqtrim/0.9 None application computational biology fqtrim: trimming & filtering of NGS reads.
freebayes 1.2.0 freebayes/1.2 None application Biology Bayesian haplotype-based polymorphism discovery and genotyping
freebayes 1.3.1 freebayes/1.3 None application Biology Bayesian haplotype-based polymorphism discovery and genotyping
freesurfer 5.3.0 freesurfer/5.3 None application computational neuroimaging An open source software suite for processing and analyzing (human) brain MRI images.
freesurfer 6.0.0 freesurfer/6.0 None application computational neuroimaging An open source software suite for processing and analyzing (human) brain MRI images.
gapfiller 2.1.1 gapfiller/2.1 None application computational biology GapFiller is a seed-and-extend local assembler to fill the gap within paired reads.
gatk4 4.0.4.0 gatk4/4.0 None application computational biology GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gatk4 4.1.2.0 gatk4/4.1 None application computational biology GATK4: This toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping.
gaussian 09 RevD gaussian/09/RevD None application Chemistry
gaussian 09 RevE gaussian/09/RevE None application Chemistry
gaussian 16 RevE gaussian/16/RevA None application Chemistry
gbmunge 2018.07.06 gbmunge/2018.07.06 None application computational biology Munge GenBank files into FASTA and tab-separated metadata.
gdcclient 1.3.0 gdcclient/1.3 None application genomics GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
gdcclient 1.4.0 gdcclient/1.4 None application genomics GDC provides a standard client-based mechanism in support of high performance data downloads and submission.
gem 2.7 gem/2.7 None application computational biology GEM: High resolution peak calling and motif discovery for ChIP-seq and ChIP-exo data.
genometools/py27 1.5.10 genometools/py27/1.5 None application Bioinformatics GenomeTools genome analysis system.
genometools/py35 1.5.10 genometools/py35/1.5 None application Bioinformatics GenomeTools genome analysis system.
genometools/py36 1.5.10 genometools/py36/1.5 None application Bioinformatics GenomeTools genome analysis system.
gensim 3.8.0 gensim/py37/3.8 None application Machine learning Topic Modelling for Humans
gensim 3.8.0 gensim/py27/3.8 None application Machine learning Topic Modelling for Humans
gensim 3.8.0 gensim/py36/3.8 None application Machine learning Topic Modelling for Humans
geoparse 1.0.5 geoparse/1.0 None application Bioinformatics Python library to access Gene Expression Omnibus Database (GEO)
gffcompare 0.10.6 gffcompare/0.10 None application Annotation GffCompare by Geo Pertea
ghostscript 9.20 ghostscript/9.20 None library runtime support An interpreter for the PostScript language and for PDF.
ghostscript 9.22 ghostscript/9.22 None library runtime support An interpreter for the PostScript language and for PDF.
git 2.17.0 git/2.17 None library tools distributed version control system
git 2.22.0 git/2.22 None library tools distributed version control system
git 2.7.4 git/2.7 None library tools distributed version control system
globus-cli 1.10.1 globus-cli/1.10 None application tool Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases.
globus-cli 1.2.0 globus-cli/1.2 None application tool Command line clients provide an interface to Globus services from the shell, and are suited for both interactive use and simple scripting use cases.
glpk 4.61 glpk/4.61 None application mathematics The 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.
gmap 2015.12.31 gmap/2015.12.31 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap 2017.05.08 gmap/2017.05.08 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmap 2018.03.25 gmap/2018.03.25 None application computational biology GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program.
gmcloser 1.6.2 gmcloser/1.6 None application computational biology GMcloser fills and closes the gaps present in scaffold assemblies, especially those generated by the de novo assembly of whole genomes with next-generation sequencing (NGS) reads.
gnu-parallel 20180522 gnu-parallel/20180522 None application Shell tool GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
gnuplot 4.6.0 gnuplot/4.6 None application unknown Gnuplot, plotting from command line
gnuplot 5.2.3 gnuplot/5.2 None application unknown Gnuplot, plotting from command line
gradle 3.3 gradle/3.3 None application Utility Gradle is an open-source build automation tool focused on flexibility and performance.
gradle 5.6 gradle/5.6 None application Utility Gradle is an open-source build automation tool focused on flexibility and performance.
gramalign 3.0 gramalign/3.0 None application computational biology GramAlign is a time-efficient progressive Multiple Sequence Alignment (MSA) algorithm.
gramcluster 1.3 gramcluster/1.3 None application computational biology GramCluster is a fast and accurate progressive clustering algorithm that relies on a grammar-based sequence distance and is particularly useful in clustering large datasets.
gramdist 1.0 gramdist/1.0 None application computational biology GramDist is a utility for generating dissimilarity matrices using the relative complexity measure, a computationally efficient and alignment free evolutionary distance metric.
graphlan 1.0.0 graphlan/1.0 None application computational biology GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
graphlan 1.1.2 graphlan/1.1 None application computational biology GraPhlAn is a software tool for producing high-quality circular representations of taxonomic and phylogenetic trees. It focuses on concise, integrative, informative, and publication-ready representations of phylogenetically- and taxonomically-driven investigation.
graphviz 2.38.0 graphviz/2.38 None library unknown
gtdbtk 0.1.3 gtdbtk/0.1 None application computational biology A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.
gubbins 2.3.4 gubbins/2.3 None application Biology Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins.
gurobi-python 8.1.0 gurobi-python/py35/8.1 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi-python 8.1.0 gurobi-python/py36/8.1 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
gurobi-python 8.1.0 gurobi-python/py27/8.1 None application Mathematics The Gurobi Optimizer is the state-of-the-art math programming solver able to handle all major problem types.
halla 0.8.17 halla/0.8 None application computational biology HAllA: Hierarchically All-against-All Association Testing.
hdf5 1.10 hdf5/1.10 compiler/gcc/9.1 compiler/pgi/19 compiler/intel/19 library runtime support
hipmcl 1.6 hipmcl/1.6 compiler/gcc/9.1:openmpi/4.0 application network clustering HipMCL is a high-performance parallel algorithm for large-scale network clustering.
hisat2 2.0.5 hisat2/2.0 None application computational biology graph-based alignment of next generation sequencing reads to a population of genomes
hisat2 2.1.0 hisat2/2.1 None application computational biology graph-based alignment of next generation sequencing reads to a population of genomes
hotspot3d 0.6.0 hotspot3d/0.6 None application bioinformatics This 3D proximity tool can be used to identify mutation hotspots from linear protein sequence and correlate the hotspots with known or potentially interacting domains, mutations, or drugs. Mutation-mutation and mutation-drug clusters can also be identified and viewed.
htseq 0.11.2 htseq/py27/0.11 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.11.2 htseq/py36/0.11 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.11.2 htseq/py37/0.11 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.5.4p5 htseq/0.5.4p5 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.6.1p1 htseq/0.6.1p1 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htseq 0.9.1 htseq/0.9 None application computational biology HTSeq - Analysing high-throughput sequencing data with Python
htslib 1.7 htslib/1.7 None application computational biology HTSlib is an implementation of a unified C library for accessing common file formats.
htstream e919d21 htstream/e919d21 None application Bioinformatics A toolset for high throughput sequence analysis using a streaming approach facilitated by Linux pipes.
humann2 0.11.2 humann2/0.11 None application computational biology HUMAnN2 is the HMP Unified Metabolic Analysis Network 2
humann2 0.9.9 humann2/0.9 None application computational biology HUMAnN2 is the HMP Unified Metabolic Analysis Network 2
ima3 1.0 ima3/1.0 None application Phylogeny IMa3 provides for estimation of the posterior probability of the population phylogenetic topology by using a new kind of data augmentation called a 'hidden genealogy'.
imagemagick 7.0.8_10 imagemagick/7.0 None application bitmap Software suite to create, edit, compose, or convert bitmap images.
imbalanced-learn-gpu 0.4.3 imbalanced-learn-gpu/py36/0.4 None application Machine Learning Python module to balance data set using under- and over-sampling
imbalanced-learn-gpu 0.4.3 imbalanced-learn-gpu/py37/0.4 None application Machine Learning Python module to balance data set using under- and over-sampling
impute2 2.3.2 impute2/2.3 None application computational biology IMPUTE2 is a computer program for phasing observed genotypes and imputing missing genotypes.
intel-mkl 19 intel-mkl/19 None library tools Numerical library, contains blas/lapack
intel-mpi 19 intel-mpi/19 compiler/intel/19 library runtime support
iqtree 1.6.7 iqtree/1.6 None application computational biology IQ-TREE creates phylogenetic trees under maximum likelihood with emphasis on speed and accuracy.
jamm 1.0.7r2 jamm/1.0.7r2 None application computational biology JAMM is a peak finder for NGS datasets (ChIP-Seq, ATAC-Seq, DNase-Seq..etc.) that can integrate replicates and assign peak boundaries accurately.
jasper 2.0 jasper/2.0 compiler/pgi/19 compiler/gcc/9.1 compiler/intel/19 library runtime support
java 1.6 java/1.6 None application system Java JDK.
java 1.7 java/1.7 None application system Java JDK.
java 1.8 java/1.8 None application system Java JDK.
java 11 java/11 None application system Java JDK.
java 12 java/12 None application system Java JDK.
jq 1.6 jq/1.6 None application Utility A command-line JSON processor.
julia 1.0 julia/1.0 None application Language A high-performance dynamic programming language for data science
julia 1.1.1 julia/1.1 None application Language A high-performance dynamic programming language for data science
justorthologs 0.0.20190308 justorthologs/0.0.20190308 None application Biology JustOrthologs: a fast, accurate and user-friendly ortholog identification algorithm.
jvarkit-msa2vcf 1.0 jvarkit-msa2vcf/1.0 None application computational biology Getting a VCF file from a CLUSTAW or a FASTA alignment.
jvarkit-sam2tsv 1.0 jvarkit-sam2tsv/1.0 None application computational biology Prints the SAM alignments as a TAB delimited file.
jvarkit-vcf2bam 2018.04.05 jvarkit-vcf2bam/2018.04.05 None application computational biology Converts VCF to BAM files
kalign 2.0 kalign/2.0 None application computational biology Kalign is a fast and accurate multiple sequence alignment algorithm designed to align large numbers of protein sequences.
keras 2.2.4 keras/py27/2.2 None application machine learning Deep Learning Library for Theano and TensorFlow
keras 2.2.4 keras/py36/2.2 None application machine learning Deep Learning Library for Theano and TensorFlow
kneaddata 0.7.2 kneaddata/0.7 None application computational biology KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
kronos 2.3.0 kronos/2.3 None application workflow Kronos is a highly flexible Python-based software tool that mainly enables bioinformatics developers, i.e. bioinformaticians who develop workflows for analyzing genomic data, to quickly make a workflow.
ksnp 3.1 ksnp/3.1 None application computational biology kSNP identifies the pan-genome SNPs in a set of genome sequences, and estimates phylogenetic trees based upon those SNPs.
lammps 05Jun2019 lammps/05Jun2019 compiler/gcc/9.1:openmpi/4.0 compiler/intel/19:openmpi/4.0 compiler/pgi/19:openmpi/4.0 library runtime support
lefse 1.0.8.post1 lefse/1.0 None application computational biology LEfSe (Linear discriminant analysis Effect Size) determines the features (organisms, clades, operational taxonomic units, genes, or functions) most likely to explain differences between classes by coupling standard tests for statistical significance with additional tests encoding biological consistency and effect relevance.
lftp 4.8.3 lftp/4.8 None application system LFTP is a sophisticated file transfer program supporting a number of network protocols (ftp, http, sftp, fish, torrent).
lmod None lmod None unknown unknown Lmod: An Environment Module System
logomaker 0.8 logomaker/py36/0.8 None application Utility Package for making Sequence Logos
logomaker 0.8 logomaker/py27/0.8 None application Utility Package for making Sequence Logos
lynx 2.8.8 lynx/2.8 None application tool Lynx is a text browser for the World Wide Web.
lyve-set 2.0.1 lyve-set/2.0 None application computational biology LYVE version of the Snp Extraction Tool (SET), a method of using hqSNPs to create a phylogeny.
maaslin 0.0.5 maaslin/0.05 None application computational biology MaAsLin is a multivariate statistical framework that finds associations between clinical metadata and microbial community abundance or function.
maaslin2 0.3.0 maaslin2/0.3 None application computational biology MaAsLin2 is comprehensive R package for efficiently determining multivariable association between microbial meta'omic features and clinical metadata.
macs2 2.1.1 macs2/2.1 None application computational biology MACS -- Model-based Analysis of ChIP-Seq
mafft 7.407 mafft/7.407 None application Bioinformatics Multiple alignment program for amino acid or nucleotide sequences based on fast Fourier transform
maker 2.31.10 maker/2.31 None application computational biology MAKER is a genome annotation pipeline for prokaryotic and smaller eukaryotic organisms.
mapping-iterative-assembler 1.0 mapping-iterative-assembler/1.0 None application bioinformatics Consensus calling or `reference assisted assembly`, chiefly of ancient mitochondria.
mapsplice 2.2.0 mapsplice/2.2 None application computational biology MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations.
mashmap 2.0 mashmap/2.0 None application computational biology A fast approximate aligner for long DNA sequences
masurca 3.3.1 masurca/3.3 None application Biology MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. MaSuRCA requires Illumina data, and supports third-generation PacBio/Nanopore MinION reads for hybrid assembly.
mathematica 10.0 mathematica/10.0 None unknown unknown
mathematica 10.4 mathematica/10.4 None unknown unknown
mathematica 11.0 mathematica/11.0 None unknown unknown
mathematica 11.3 mathematica/11.3 None unknown unknown
mathematica 9.0 mathematica/9.0 None unknown unknown
matlab r2012b matlab/r2012b None unknown unknown
matlab r2013b matlab/r2013b None unknown unknown
matlab r2014b matlab/r2014b None unknown unknown
matlab r2015b matlab/r2015b None unknown unknown
matlab r2016a matlab/r2016a None unknown unknown
matlab r2016b matlab/r2016b None unknown unknown
matlab r2017a matlab/r2017a None unknown unknown
matlab r2017b matlab/r2017b None unknown unknown
matlab r2018a matlab/r2018a None unknown unknown
matlab r2018b matlab/r2018b None unknown unknown
matlab r2019a matlab/r2019a None unknown unknown
maxquant 1.6.6.0 maxquant/1.6 None application biochemistry MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets.
mbuffer 20171011 mbuffer/20171011 None application buffer Mbuffer is a tool for buffering data streams with a large set of unique features.
mcl 14.137 mcl/14.137 None application computational biology MCL
megahit 1.1 megahit/1.1 None application computational biology MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
megahit 1.2.8 megahit/1.2 None application computational biology MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
megan 6.12.3 megan/6.12 None application Computational Biology A tool for studying the taxonomic content of a set of DNA reads
melonnpan 2019.03.22 melonnpan/2019.03.22 None application computational biology MelonnPan is a computational method for predicting metabolite compositions from shotgun metagenomic sequencing data.
metaphlan2 2.6.0 metaphlan2/2.6 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metaphlan2 2.7.8 metaphlan2/2.7 None application metagenomic phylogenetic analysis MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data.
metasv 0.5.4 metasv/0.5 None application computational biology An accurate and integrative structural-variant caller for next generation sequencing.
metawrap 1.1 metawrap/1.1 None application computational biology MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
metawrap 1.2 metawrap/1.2 None application computational biology MetaWRAP is a pipeline for genome-resolved metagenomic data analysis
micropita 1.1.0 micropita/1.1 None application computational biology microPITA is a computational tool enabling sample selection in two-stage (tiered) studies.
midnight-commander 4.8.22 midnight-commander/4.8 None application Utility GNU Midnight Commander is a visual file manager, licensed under GNU General Public License and therefore qualifies as Free Software. It's a feature rich full-screen text mode application that allows you to copy, move and delete files and whole directory trees, search for files and run commands in the subshell. Internal viewer and editor are included.
minimap2 2.16 minimap2/2.16 None application bioinformatics A versatile pairwise aligner for genomic and spliced nucleotide sequences.
mlpack 2.2.5 mlpack/2.2 None application Machine Learning mlpack a fast, flexible machine learning library
mlpack 3.0.3 mlpack/3.0 None application Machine Learning mlpack a fast, flexible machine learning library
mlst 2.16.2 mlst/2.16 None application computational biology Scan contig files against PubMLST typing schemes
morgan 3.4 morgan/3.4 None application computational biology MORGAN is part of our software for Markov chain Monte Carlo in Genetic Analysis.
mosdepth 0.2.4 mosdepth/0.2 None application computational biology Fast BAM/CRAM depth calculation for WGS, exome, or targetted sequencing.
mothur 1.41.3 mothur/1.41 None application Bioinformatics This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
mspkmercounter 0.10.0 mspkmercounter/0.10 None application Biology MSPKmerCounter is a k-mer counter based on the minimum substring partitioning technique.
multigps 0.74 multigps/0.74 None application computational biology MultiGPS is a framework for analyzing collections of multi-condition ChIP-seq datasets and characterizing differential binding events between conditions.
multiqc 1.6 multiqc/py36/1.6 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc 1.6 multiqc/py27/1.6 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
multiqc 1.6 multiqc/py35/1.6 None application computational biology MultiQC is a tool to create a single report with interactive plots for multiple bioinformatics analyses across many samples.
mummer4 4.0.0beta2 mummer4/4.0 None application Bioinformatics MUMmer is a system for rapidly aligning entire genomes
mxnet 0.9.3a mxnet/0.9.3 None application AI MXNet 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.
mxnet 1.5.0 mxnet/1.5 None application AI MXNet 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.
nano 2.9.8 nano/2.9 None application Utility Nano's ANOther editor, an enhanced free Pico clone
ncbi-download 0.2.6 ncbi-download/0.2 None application computational biology Python scriopt for downloading bacterial and fungal genomes from NCBI.
ncl 6.6.2 ncl/6.6 None application utility NCAR Command Language
nco 4.8.1 nco/4.8 None library runtime support Suite of programs for manipulating NetCDF/HDF4 files.
neper 3.3.0 neper/3.3 None application Applications Neper is a software package for polycrystal generation and meshing.
neptune 1.2.5 neptune/1.2 None application computational biology Neptune locates genomic signatures using an exact k-mer matching strategy while accommodating k-mer mismatches.
netcdf 4.7 netcdf/4.7 compiler/pgi/19 compiler/gcc/9.1 compiler/intel/19 library runtime support
netcdf-c 4.7 netcdf-c/4.7 compiler/intel/19 compiler/gcc/9.1 compiler/pgi/19 library runtime support
netcdf-cxx4 4.3 netcdf-cxx4/4.3 compiler/pgi/19 compiler/intel/19 compiler/gcc/9.1 library runtime support
netcdf-fortran 4.4 netcdf-fortran/4.4 compiler/gcc/9.1 compiler/pgi/19 compiler/intel/19 library runtime support
nwchem 6.8 nwchem/6.8 compiler/intel/19:openmpi/4.0 library runtime support
octave 4.2 octave/4.2 None application engineering GNU 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.
oncotator 1.9.9.0 oncotator/1.9 None application computational biology Oncotator is a tool for annotating human genomic point mutations and indels with data relevant to cancer researchers.
opencv 3.4.1 opencv/py27/3.4 None library unknown OpenCV is a computer vision and machine learning software library.
opencv 3.4.1 opencv/py36/3.4 None library unknown OpenCV is a computer vision and machine learning software library.
openmpi 4.0 openmpi/4.0 compiler/gcc/9.1 compiler/intel/19 compiler/pgi/19 library runtime support
orthofinder 1.1.8 orthofinder/1.1 None application computational biology OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
orthofinder 2.2.6 orthofinder/2.2 None application computational biology OrthoFinder is a fast, accurate and comprehensive analysis tool for comparative genomics.
orthomcl 2.0.9 orthomcl/2.0 None application Biology Ortholog groups of protein sequences
paml 4.9 paml/4.9 None application Sequencing Phylogenetic Analysis by Maximum Likelihood (PAML)
pandaseq 2.11 pandaseq/2.11 None application bioinformatics PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
peakranger 1.18 peakranger/1.18 None application computational biology PeakRanger is a multi-purporse software suite for analyzing next-generation sequencing (NGS) data.
peakzilla 1.0 peakzilla/1.0 None application computational biology Peakzilla identifies sites of enrichment and transcription factor binding sites from transcription factor ChIP-seq and ChIP-exo experiments at hight accuracy and resolution.
pepr 1.1.18 pepr/1.1 None application computational biology Peak-calling and Prioritization pipeline for replicated ChIP-Seq data.
perl 5.22 perl/5.22 None application perl The Perl Programming Language
perl 5.26.2 perl/5.26 None application perl The Perl Programming Language
phylogenetics 0.5.0 phylogenetics/0.5 None application computational biology Python API for managing a phylogenetics projects.
phylophlan 1.0 phylophlan/1.0 None application computational biology PhyloPhlAn is a computational pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information.
phylosnp 1.0 phylosnp/1.0 None application computational biology PhyloSNP is designed to take SNP data files (.csv and .vcf) and generate phylogenetic trees from the provided data.
phyml 3.3.20180621 phyml/3.3 None application Biology Phylogenetic estimation using (Maximum) Likelihood
picard 2.18.4 picard/2.18 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
picard 2.9.0 picard/2.9 None application computational biology A set of Java command line tools for manipulating high-throughput sequencing data (HTS) data and formats.
pilon 1.23 pilon/1.23 None application bioinformatics Pilon is an automated genome assembly improvement and variant detection tool.
pindel 0.2.5b9 pindel/0.2 None application computational biology
pirs 2.0.2 pirs/2.0 None application computational biology
plasmidfinder 2.0.1 plasmidfinder/2.0 None application computational biology PlasmidFinder allows identification of plasmids in total or partial sequenced isolates of bacteria.
plink 1.90b4 plink/1.90 None application computational biology PLINK 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.
plink2 2.0a1 plink2/2.0a1 None application computational biology This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab at Mount Sinai School of Medicine, and others.
plinkseq 0.10 plinkseq/0.10 None application computational biology PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data.
pomoxis 0.1.7 pomoxis/0.1 None application computational biology Pomoxis comprises APIs and command line tools for interacting and analysing Oxford Nanopore Technologies data in real time.
poppunk 1.1.6 poppunk/1.1 None application computational biology PopPUNK (POPulation Partitioning Using Nucleotide Kmers)
prokka 1.12 prokka/1.12 None application bioinformatics Prokka is a software tool for the rapid annotation of prokaryotic genomes.
prokka 1.13.7 prokka/1.13 None application bioinformatics Prokka is a software tool for the rapid annotation of prokaryotic genomes.
proteowizard 3_0_9992 proteowizard/3.0 None application computational biology ProteoWizard provides a modular and extensible set of open-source, cross-platform tools and libraries.
pullseq 1.0 pullseq/1.0 None application computational biology pullseq - Software to extract sequence from a fasta or fastq. Also filter sequences by a minimum length or maximum length.
pyclone 0.13 pyclone/0.13 None application computational biology PyClone is statistical model and software tool designed to infer the prevalence of point mutations in heterogeneous cancer samples.
pyfasta 0.5 pyfasta/0.5 None application computational biology Pyfasta - fast, memory-efficient, pythonic (and command-line) access to fasta sequence files.
pygenometracks 2.0 pygenometracks/2.0 None application bioinformatics Standalone program and library to plot beautiful genome browser tracks.
pymongo 3.0.3 pymongo/3.0 None application Utility PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pymongo 3.3.0 pymongo/3.3 None application Utility PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pymongo 3.7.2 pymongo/3.7 None application Utility PyMongo is a Python distribution containing tools for working with MongoDB, and is the recommended way to work with MongoDB from Python.
pyseer 1.2.0 pyseer/1.2 None application computational biology Sequence Elements Enrichment Analysis (SEER), python implementation
python 2.7 python/2.7 None application system
python 3.4 python/3.4 None application system
python 3.5 python/3.5 None application system
python 3.6 python/3.6 None application system
python 3.7 python/3.7 None application system
pytorch 0.4.1 pytorch/py27/0.4 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 0.4.1 pytorch/py36/0.4 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
pytorch 0.4.1 pytorch/py35/0.4 None application deep learning PyTorch is an optimized tensor library for deep learning using GPUs and CPUs.
qiime2 2018.4 qiime2/2018.4 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
qiime2 2019.1 qiime2/2019.1 None application computational biology QIIME 2 is a powerful, extensible, and decentralized microbiome analysis package with a focus on data and analysis transparency.
quasr 6.09 quasr/6.09 None application computational biology QUASR is lightweight pipeline for processing and analysis of high-throughput sequencing data.
quast 4.4 quast/4.4 None application computational biology QUAST evaluates genome assemblies by computing various metrics.
quast 4.5 quast/4.5 None application computational biology QUAST evaluates genome assemblies by computing various metrics.
quast 5.0 quast/5.0 None application computational biology QUAST evaluates genome assemblies by computing various metrics.
r-asreml 4.1 r-asreml/r34/4.1 None application data analysis ASReml-R is a statistical package that fits linear mixed models using Residual Maximum Likelihood (REML) in the R environment.
r-genometricorr 1.1.17 r-genometricorr/1.1 None application Genomics Genometric Correlation (GenometriCorr) is an R package for spatial correlation of genome-wide interval datasets.
r-ggfortify 0.4.1 r-ggfortify/0.4 None application r ggfortify is a package of unified plotting tools for statistics commonly used, such as GLM, time series, PCA families, clustering and survival analysis.
r-keras 2.2.4.1 r-keras/2.2 None application machine learning Interface to 'Keras' <https://keras.io>, a high-level neural networks 'API'.
r-markdown 0.8 r-markdown/0.8 None application R Markdown is a plain-text formatting syntax that can be converted to XHTML or other formats.
r-regresshaplo 1.0 r-regresshaplo/1.0 None application biology This package reconstructs haplotypes from a BAM file using a penalized regression approach.
r-rhierbaps 1.1.2 r-rhierbaps/1.1 None application computational biology rhierbaps is R implementation of hierBAPS.
r-scimpute 0.0.6 r-scimpute/0.0.6 None application biology scImpute is accurate and robust imputation of single-cell RNA sequencing data.
r-seqminer 6.0 r-seqminer/6.0 None application biology SEQMINER is for sequencing variant annotation, data integration and query in R.
r-vcfr 1.5.0 r-vcfr/1.5 None application biology A package to manipulate and visualize VCF data in R.
rarefactionanalyzer 2018.09.06 rarefactionanalyzer/2018.09.06 None application computational biology Rarefaction analyzer is a simple program that can be used to perform rarefaction analysis.
raxml 8.2.12 raxml/8.2 None application Biology Phylogenetics - Randomized Axelerated Maximum Likelihood.
rclone 1.44 rclone/1.44 None application Storage Rclone - rsync for cloud storage.
red 2015.05.22 red/2015.05.22 None application Genomics Red (RepeatsDetector): an intelligent, rapid, accurate tool for detecting repeats de-novo on the genomic scale.
regtools 0.5.0 regtools/0.5 None application bioinformatics Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context.
repenrich 1.2 repenrich/1.2 None application computational biology RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
resistomeanalyzer 2018.09.06 resistomeanalyzer/2018.09.06 None application computational biology Resistome Analyzer is a simple tool for analyzing the resistome of large metagenomic datasets.
revtrans 1.4 revtrans/1.4 None application computational biology RevTrans - performs a reverse translation of a peptide alignment.
rgi 5.0.0 rgi/5.0 None application computational biology Resistance gene identifier.
rgt 0.11.4 rgt/0.11 None application computational biology Toolkit to perform regulatory genomics data analysis
rhino None rhino None unknown unknown
ripser 1.0.1 ripser/1.0 None application Bioinformatics Ripser: efficient computation of VietorisRips persistence barcodes.
rnaquast 1.5.1 rnaquast/1.5 None application Biology rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software.
rnastructure 6.1 rnastructure/6.1 None application Bioinformatics RNAstructure is a complete package for RNA and DNA secondary structure prediction and analysis. It includes algorithms for secondary structure prediction, including facility to predict base pairing probabilities. It also can be used to predict bimolecular structures and can predict the equilibrium binding affinity of an oligonucleotide to a structured RNA target. This is useful for siRNA design. It can also predict secondary structures common to two, unaligned sequences, which is much more accurate than single sequence secondary structure prediction. Finally, RNAstructure can take a number of different types of experiment mapping data to constrain or restrain structure prediction. These include chemical mapping, enzymatic mapping, NMR, and SHAPE data.
roary 3.12.0 roary/3.12 None application computational biology Rapid large-scale prokaryote pan genome analysis
rsem 1.3 rsem/1.3 None application computational biology RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data.
salmon 0.6.0 salmon/0.6 None application computational biology Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon 0.8.2 salmon/0.8 None application computational biology Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
salmon 0.9.1 salmon/0.9 None application computational biology Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments.
samtools 1.5 samtools/1.5 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.6 samtools/1.6 None application computational biology Tools for dealing with SAM, BAM and CRAM files
samtools 1.9 samtools/1.9 None application computational biology Tools for dealing with SAM, BAM and CRAM files
sas 9.4 sas/9.4 None application Applications SAS is a software suite developed by SAS Institute for advanced analytics, business intelligence, data management, and predictive analytics.
scoary 1.6.16 scoary/py27/1.6 None application computational biology Microbial pan-GWAS using the output from Roary
scoary 1.6.16 scoary/py36/1.6 None application computational biology Microbial pan-GWAS using the output from Roary
scoary 1.6.16 scoary/py35/1.6 None application computational biology Microbial pan-GWAS using the output from Roary
scons 2.5 scons/2.5 None application utility SCons: A software construction tool.
scons 3.0 scons/3.0 None application utility SCons: A software construction tool.
seedme 1.2 seedme/1.2 None application Utility Client program for SeedMe.org.
selecton 2.4 selecton/2.4 None application Bioinformatics Selecton 2007: advanced models for detecting positive and purifying selection using a Bayesian inference approach.
seqkit 0.10.1 seqkit/0.10 None application computational biology Cross-platform and ultrafast toolkit for FASTA/Q file manipulation
seqtk 1.2 seqtk/1.2 None application computational biology Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format.
seqyclean 1.10.07 seqyclean/1.10 None application Bioinformatics Main purpose of this software is to pre-process NGS data in order to prepare for downstream analysis.
settarg None settarg None unknown unknown
shapeit 2.0 shapeit/2.0 None application computational biology SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data.
shortstack 3.8.5 shortstack/3.8 None application Biology ShortStack: Comprehensive annotation and quantification of small RNA genes
shovill 1.0.4 shovill/1.0 None application computational biology Microbial assembly pipeline for Illumina paired-end reads
sift4g 2.0.0 sift4g/2.0 None application computational biology SIFT 4G is a faster version of SIFT that enables us to scale up and provide SIFT predictions for more organisms.
singularity 3.2 singularity/2.3 None application system Application containers enabling mobility of compute.
singularity 3.2 singularity/2.2 None application system Application containers enabling mobility of compute.
singularity 3.2 singularity/3.2 None application system Application containers enabling mobility of compute.
singularity 3.2 singularity/2.6 None application system Application containers enabling mobility of compute.
singularity 3.2 singularity/2.4 None application system Application containers enabling mobility of compute.
sistr_cmd 1.0.2 sistr_cmd/1.0 None application computational biology
smrtlink 5.1.0.26412 smrtlink/5.1 None application Biology PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
smrtlink 7.0.1.66975 smrtlink/7.0 None application Biology PacBio's open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data.
snippy 4.3.6 snippy/4.3 None application computational biology Rapid bacterial SNP calling and core genome alignments
snp-pipeline 0.7 snp-pipeline/0.7 None application computational biology Script and functions for SNP matrix construction
snp-pipeline 1.0 snp-pipeline/1.0 None application computational biology Script and functions for SNP matrix construction
snp-pipeline 2.0.2 snp-pipeline/2.0 None application computational biology Script and functions for SNP matrix construction
snp-sites 2.3.3 snp-sites/2.3 None application computational biology SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.
snp-sites 2.4.1 snp-sites/2.4 None application computational biology SNP-sites rapidly extracts SNPs from a multi-FASTA alignment.
snpeff 4.3 snpeff/4.3 None application computational biology Genetic variant annotation and effect prediction toolbox.
snpfinder 1.0.0 snpfinder/1.0 None application computational biology SNPFinder is a simple alignment-based haplotype variant caller that can be used with metagenomic sequence data.
soapdenovo-trans 1.04 soapdenovo-trans/1.04 None application computational biology SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts.
sonnet 1.13 sonnet/py35/1.13 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.13 sonnet/py27/1.13 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.13 sonnet/py36/1.13 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.19 sonnet/py27/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.19 sonnet/py35/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.19 sonnet/py36/1.19 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.23 sonnet/py36/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.23 sonnet/py27/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.23 sonnet/py35/1.23 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.27 sonnet/py36/1.27 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
sonnet 1.27 sonnet/py27/1.27 None application machine learning Sonnet is a library built on top of TensorFlow for building complex neural networks.
spades 3.10.1 spades/3.10 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.11.1 spades/3.11 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.12.0 spades/3.12 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.13.0 spades/py35/3.13 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.13.0 spades/py27/3.13 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.13.0 spades/py36/3.13 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
spades 3.8.1 spades/3.8 None application computational biology SPAdes - St. Petersburg genome assembler - is intended for both standard isolates and single-cell MDA bacteria assemblies.
sparcc 0.1.0 sparcc/py27/0.1 None application computational biology SparCC is a python module for computing correlations in compositional data (16S, metagenomics, etc).
spython 0.0.69 spython/0.0.69 None application singularity Command line python tool for working with singularity.
ssake 4.0 ssake/4.0 None application genomics SSAKE is a genomics application for de novo assembly of millions of very short DNA sequences.
stacks 2.4 stacks/2.4 None application computational biology Stacks is a software pipeline for building loci from RAD-seq
stamp 2.1.3 stamp/2.1 None application Taxonomy A graphical software package for analyzing taxonomic and functional profiles.
star 2.7.1a star/2.7 None application biology An RNA-seq read aligner.
stereogene 2.20 stereogene/2.20 None application sequencing StereoGene: Rapid Estimation of Genomewide Correlation of Continuous or Interval Feature Data
strelka 2.9.10 strelka/2.9 None application computational biology Strelka calls somatic and germline small variants from mapped sequencing reads
structure 2.3.4 structure/2.3 None application computational biology 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. It can be applied to most of the commonly-used genetic markers, including SNPS, microsatellites, RFLPs and AFLPs.
szip 2.1 szip/2.1 compiler/pgi/19 compiler/gcc/9.1 compiler/intel/19 library runtime support
targetfinder 1.7 targetfinder/1.7 None application computational biology Plant small RNA target prediction tool.
tassel 5.2.40 tassel/5.2 None application computational biology TASSEL is a software package to evaluate traits associations, evolutionary patterns, and linkage disequilibrium.
tax2tree 1.0 tax2tree/1.0 None application computational biology tax2tree - Tools for decorating taxonomy information on to a phylogenetic tree.
tensorflow 1.11.0 tensorflow/py36/1.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.11.0 tensorflow/py27/1.11 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.12.0 tensorflow/py27/1.12 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.12.0 tensorflow/py36/1.12 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.14.0 tensorflow/py36/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.14.0 tensorflow/py37/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
tensorflow 1.14.0 tensorflow/py27/1.14 None application machine learning TensorFlow is an open source software library for numerical computation using data flow graphs.
theano 0.9.0 theano/py36/0.9 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 0.9.0 theano/py35/0.9 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 0.9.0 theano/py27/0.9 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 1.0.3 theano/py36/1.0 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 1.0.3 theano/py35/1.0 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
theano 1.0.3 theano/py27/1.0 None application mathematics Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
tophat 2.1.1 tophat/2.1 None application computational biology TopHat2 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.
transdecoder 3.0.1 transdecoder/3.0 None application computational biology TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks.
treemix 1.13 treemix/1.13 None application computational biology TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations.
triform2 0.0.5 triform2/0.0.5 None application computational biology Improved sensitivity, specificity and control of false discovery rates in ChIP-Seq peak finding.
trim_galore 0.4.5 trim_galore/0.4 None application computational biology Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control
trim_galore 0.6.4 trim_galore/0.6 None application computational biology Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control
trimmomatic 0.36 trimmomatic/0.36 None application computational biology A flexible read trimming tool for Illumina NGS data
trimmomatic 0.38 trimmomatic/0.38 None application computational biology A flexible read trimming tool for Illumina NGS data
trinity 2.4.0 trinity/2.4 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.6.6 trinity/2.6 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
trinity 2.8.4 trinity/2.8 None application computational biology Trinity RNA-Seq de novo transcriptome assembly
ucsc-fatotwobit 377 ucsc-fatotwobit/377 None application computational biology Convert DNA from fasta to 2bit format
ucsc-liftover 366 ucsc-liftover/366 None application computational biology The Batch Coordinate Conversion (liftOver) utility converts genome coordinates and genome annotation files between assemblies.
ucsc-twobittofa 357 ucsc-twobittofa/357 None application computational biology Convert all or part of .2bit file to fasta
ucsc-twobittofa 377 ucsc-twobittofa/377 None application computational biology Convert all or part of .2bit file to fasta
udunits2 2.2 udunits2/2.2 compiler/pgi/19 compiler/intel/19 compiler/gcc/9.1 library runtime support
unicycler 0.4.7 unicycler/0.4 None application bioinformatics Hybrid assembly pipeline for bacterial genomes
usearch 11.0.667 usearch/11.0 None application computational biology USEARCH is a unique sequence analysis tool with thousands of users world-wide.
varscan 2.4.3 varscan/2.4 None application computational biology Variant calling and somatic mutation/CNV detection for next-generation sequencing data
vasp 5.4.4 vasp/5.4 compiler/intel/19:openmpi/4.0 library runtime support
velvetoptimiser 2.2.6 velvetoptimiser/2.2 None application computational biology Automatically optimise three of Velvet's assembly parameters.
viennarna 2.3.3 viennarna/2.3 None application computational biology The ViennaRNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
vim 8.1.0960 vim/8.1 None application Utility Vim is a greatly improved version of the good old UNIX editor Vi
visit 2.10.2 visit/2.10 None application utility VisIt is an Open Source, interactive, scalable, visualization, animation and analysis tool.
vsearch 2.10.0 vsearch/2.10 None application computational biology A versatile open source tool for metagenomics (USEARCH alternative)
weblogo 3.7.4 weblogo/3.7 None application Utility WebLogo3 : Sequence Logos Redrawn
xcrysden 1.5.60 xcrysden/1.5 None application physics XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated.
zerone 1.0 zerone/1.0 None application computational biology Zerone 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.
zlib 1.2 zlib/1.2 compiler/pgi/19 compiler/intel/19 compiler/gcc/9.1 library runtime support
zorro 2011.12.01 zorro/2011.12.01 None application bioinformatics ZORRO is a probabilistic masking program that assigns confidence scores to each column in a multiple sequence alignment.