Scientific Software Modules

Updated: September 17, 2020

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On the command line and in scripts, we use the Environment Module system to make software versions available in a modular and malleable way. Environment Modules provide modular access to one version of one or more software packages to help improve reproducibility. We use a system called EasyBuild to create modules for everyone to use - there are over a thousand modules already available. The modules listed here are the software modules available currently on the gizmo compute cluster. You can read more about how to use these modules and manage your compute environment on our Compute Environments page.

R Modules

Specific information about which R Modules are available, including more information about packages installed in them can be found on our dedicated R Module page.

Python Modules

Specific information about which Python Modules are available, including more information about packages installed in them can be found on our dedicated Python Module page.

Life Science/Bio Software Modules

Other software for life sciences that are available as modules can be found below. If you do not see the software you are looking for, email scicomp to request it or add your own GitHub issue in the easybuild-life-sciences repo. Either way, please be specific about the source and version of the software you are interested in.

  • AdapterRemoval/2.2.2-foss-2018b AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3’ end of reads following adapter removal.
  • BBMap/38.79-GCC-8.3.0 BBMap short read aligner, and other bioinformatic tools.
  • BCFtools/1.9-foss-2018b easyconfig Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools
  • BEDOPS/2.4.35-foss-2018b easyconfig BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
  • BEDTools/2.29.2-GCC-8.3.0 BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM.
  • BLAST+/2.10.0-gompi-2019b easyconfig Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences.
  • BLAT/3.5-foss-2018b BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.
  • BUStools/0.40.0-foss-2019b easyconfig bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.
  • BWA/0.7.17-GCC-8.3.0 Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome.
  • BamTools/2.5.1-foss-2019b easyconfig BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.
  • Beast/2.6.2-GCCcore-8.3.0 easyconfig BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability.
  • BioPerl/1.7.2-foss-2018b-Perl-5.28.0 Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects.
  • Biopython/1.77-foss-2020a-Python-3.8.2 easyconfig Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics.
  • Bowtie/1.2.2-foss-2018b Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome.
  • Bowtie2/2.4.1-GCCcore-8.3.0 Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes.
  • CD-HIT/4.8.1-foss-2019b easyconfig CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences.
  • CITE-seq-Count/1.4.2-foss-2018b-Python-3.6.6 easyconfig A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment.
  • CNVkit/0.9.7-foss-2019b-Python-3.7.4-R-3.6.2 easyconfig A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing.
  • CRISPRCasTyper/1.2.1-foss-2020a-Python-3.8.2 easyconfig Detect CRISPR-Cas genes and arrays, and predict the subtype based on both Cas genes and CRISPR repeat sequence.
  • CellRanger/4.0.0 easyconfig Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq data produced by the 10x Genomics Chromium Platform. Output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
  • Cgl/0.60.3-GCCcore-8.3.0 easyconfig The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver.
  • Circos/0.69-6-GCCcore-7.3.0-Perl-5.28.0 Circos is a software package for visualizing data and information. It visualizes data in a circular layout
  • Clp/1.17.6-GCCcore-8.3.0 easyconfig Clp (Coin-or linear programming) is an open-source linear programming solver
  • CoinUtils/2.11.3-GCCcore-8.3.0 easyconfig CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project. A collection of routines for manipulating sparse matrices and other matrix operations
  • Control-FREEC/11.5-GCC-8.3.0 easyconfig Copy number and genotype annotation from whole genome and whole exome sequencing data.
  • Cufflinks/2.2.1-foss-2018b easyconfig Transcript assembly, differential expression, and differential regulation for RNA-Seq
  • DIAMOND/0.9.22-foss-2018b easyconfig Accelerated BLAST compatible local sequence aligner
  • EMBOSS/6.6.0-foss-2018b easyconfig EMBOSS is ‘The European Molecular Biology Open Software Suite’ EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community.
  • Eigen/3.3.7 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
  • FASTX-Toolkit/0.0.14-GCCcore-8.3.0 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing.
  • FLASH/2.2.00-foss-2018b easyconfig FLASH (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.

  • FSL/5.0.11-foss-2018b-Python-3.6.6 FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data.
  • FastANI/1.1-foss-2018b easyconfig FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies.
  • FastQC/0.11.9-Java-11 FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline.
  • FastTree/2.1.10-foss-2018b easyconfig FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory.
  • GATK/4.1.8.1-GCCcore-8.3.0-Java-11 easyconfig The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size.
  • GCTA/1.92.2beta GCTA (Genome-wide Complex Trait Analysis) was originally designed to estimate the proportion of phenotypic variance explained by all genome-wide SNPs for complex traits (the GREML method), and has subsequently extended for many other analyses to better understand the genetic architecture of complex traits.
  • GD/2.69-GCCcore-7.3.0-Perl-5.28.0 GD.pm
  • GEOS/3.8.0-GCC-8.3.0-Python-3.7.4 GEOS (Geometry Engine
  • GMAP-GSNAP/2018-07-04-foss-2018b GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program
  • GMP/6.2.0-GCCcore-9.3.0 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

  • GRIDSS/2.9.3-foss-2019b-Java-11 GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.
  • GROMACS/2018.3-foss-2018b GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles.

This is a CPU only build, containing both MPI and threadMPI builds.

  • GenomeSTRiP/2.00.1958-GCCcore-8.3.0-Java-11 Genome STRiP (Genome STRucture In Populations) is a suite of tools for discovery and genotyping of structural variation using whole-genome sequencing data. The methods used in Genome STRiP are designed to find shared variation using data from multiple individuals. Genome STRiP looks both across and within a set of sequenced genomes to detect variation.
  • HISAT2/2.1.0-foss-2018b HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome).
  • HMMER/3.2.1-foss-2018b easyconfig HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST.
  • HTSeq/0.11.0-foss-2018b-Python-2.7.15 A framework to process and analyze data from high-throughput sequencing (HTS) assays
  • HTSlib/1.10.2-GCC-8.3.0 A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
  • IDBA-UD/1.1.3-foss-2018b IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions.
  • IGV/2.8.6-Java-11 This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.
  • IGVTools/2.4.16-Java-1.8 easyconfig This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline.
  • IgBLAST/1.15.0-x64-linux easyconfig IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.
  • JAGS/4.3.0-foss-2019b easyconfig JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
  • Jellyfish/2.2.10-foss-2018b Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
  • Kent_tools/20200519-linux.x86_64 easyconfig Jim Kent’s tools: collection of tools used by the UCSC genome browser.
  • Keras/2.3.1-foss-2019b-Python-3.7.4 Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano.
  • LAST/963-foss-2018b LAST finds similar regions between sequences.
  • LoFreq/2.1.3.1-foss-2018b-Python-2.7.15 Fast and sensitive variant calling from next-gen sequencing data
  • MACS2/2.2.6-foss-2019b-Python-3.7.4 Model Based Analysis for ChIP-Seq data
  • MAFFT/7.453-GCC-8.3.0-with-extensions MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc.
  • MCR/R2019a The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed.
  • MEME/5.1.1-foss-2019b easyconfig The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo.
  • MPFR/4.0.2-GCCcore-8.3.0 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding.

  • MUMmer/4.0.0beta2-foss-2020a easyconfig MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it.
  • MUSCLE/3.8.31-foss-2018b easyconfig MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks.
  • MaxQuant/1.6.15.0-foss-2019b easyconfig MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported.
  • MethGo/24c9319-foss-2018b-Python-2.7.15 easyconfig DNA methylation is a major epigenetic modification regulating several biological processes. A standard approach in the study of DNA methylation is bisulfite sequencing (BS-Seq). MethGo is a simple and effective tool designed for the analysis of data from whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS).
  • MiXCR/3.0.3-Java-1.8 easyconfig MiXCR processes big immunome data from raw sequences to quantitated clonotypes
  • MinCED/0.4.2-GCCcore-8.3.0-Java-11 Mining CRISPRs in Environmental Datasets
  • MoreRONN/4.9-foss-2019b easyconfig MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography.
  • Mothur/1.41.0-foss-2018b-Python-2.7.15 Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
  • MultiQC/1.9-foss-2019b-Python-3.7.4 easyconfig Aggregate results from bioinformatics analyses across many samples into a single report.

MultiQC searches a given directory for analysis logs and compiles a HTML report. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools.

  • MutSig/2 easyconfig MutSig stands for “Mutation Significance”. MutSig analyzes lists of mutations discovered in DNA sequencing, to identify genes that were mutated more often than expected by chance given background mutation processes.
  • NGS/2.10.8-GCCcore-8.3.0-Java-11 easyconfig NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing.
  • OptiType/1.3.2-foss-2018b-Python-2.7.15 OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles.
  • Osi/0.108.6-GCCcore-8.3.0 easyconfig Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver.
  • PANDAseq/2.11-foss-2018b easyconfig PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence.
  • PEAR/0.9.11-foss-2018b easyconfig PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory.
  • PHASE/2.1.2-GCCcore-8.3.0 easyconfig PHASE is a program implementing the method for reconstructing haplotypes from population data
  • PLINK/2.00-alpha1-x86_64 Whole-genome association analysis toolset
  • Pindel/0.2.5b9-20170508-foss-2018b easyconfig Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
  • Porechop/0.2.4-foss-2018b-Python-3.6.6 Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity
  • Pyomo/5.5.0-foss-2018b-Python-2.7.15 Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models.
  • Pysam/0.16.0.1-GCC-9.3.0 Pysam is a python module for reading and manipulating Samfiles. It’s a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix.
  • R-bundle-Bioconductor/3.10-foss-2019b-R-3.6.2 easyconfig Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data.
  • R-keras/2.2.5.0-foss-2019b-Python-3.7.4-R-3.6.2 Interface to ‘Keras’ https://keras.io, a high-level neural networks ‘API’.
  • RNA-SeQC/2.3.4-foss-2019b easyconfig RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis.
  • ROSE/1-GCCcore-8.3.0-Python-2.7.16 easyconfig To create stitched enhancers, and to separate super-enhancers from typical enhancers using sequencing data (.bam) given a file of previously identified constituent enhancers (.gff)
  • RSEM/1.3.3-foss-2019b easyconfig RNA-Seq by Expectation-Maximization
  • RSeQC/3.0.0-foss-2018b-Python-3.6.6 easyconfig RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc.
  • RepeatMasker/4.0.8-foss-2018b-Perl-5.28.0-HMMER easyconfig RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences.
  • SAMtools/1.10-GCCcore-8.3.0 easyconfig SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
  • SKESA/2.3.0-foss-2018b SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs.
  • SPAdes/3.13.0-foss-2018b Genome assembler for single-cell and isolates data sets
  • SPRING/1.6-foss-2018b-Python-2.7.15 easyconfig SPRING is a collection of pre-processing scripts and a web browser-based tool for visualizing and interacting with high dimensional data. View an example dataset here. SPRING was developed for single cell RNA-Seq data but can be applied more generally. The minimal input is a matrix of high dimensional data points (cells) and a list of dimension names (genes).
  • SQANTI3/1.0-foss-2019b-Python-3.7.4 easyconfig SQANTI3 is the first module of the Functional IsoTranscriptomics (FIT) framework, that also includes IsoAnnot and tappAS. Used for new long read-defined transcriptome.
  • SRA-Toolkit/2.10.8-gompi-2019b The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format
  • STAR/2.7.3a-foss-2019b easyconfig STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays.
  • STAR-Fusion/1.9.0-foss-2019b-Perl-5.30.0 STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set.
  • SYMPHONY/5.6.17-GCCcore-7.3.0 easyconfig SYMPHONY is an open-source solver for mixed-integer linear programs (MILPs) written in C. It can be used in four different main modes.
  • Salmon/1.2.0-gompi-2019b easyconfig Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. Salmon achieves its accuracy and speed via a number of different innovations, including the use of selective-alignment, and massively-parallel stochastic collapsed variational inference.
  • Seaborn/0.9.0-foss-2018b-Python-3.6.6 Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics.
  • SeqAn/2.4.0-foss-2018b SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data
  • SeqPrep/1.3.2-GCCcore-8.3.0 Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  • Seqmagick/0.6.2-foss-2018b-Python-2.7.15 easyconfig We often have to convert between sequence formats and do little tasks on them, and it’s not worth writing scripts for that. Seqmagick is a kickass little utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments.
  • Sniffles/1.0.8-foss-2018b easyconfig Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.
  • Stacks/2.53-foss-2019b Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.

  • TRF/4.09-linux64 Tandem repeats finder: a program to analyze DNA sequences. Legacy version.
  • Theano/1.0.4-foss-2019b-Python-3.7.4 Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently.
  • TopHat/2.1.2-foss-2018b easyconfig TopHat is a fast splice junction mapper for RNA-Seq reads.
  • Tracer/1.7.1 easyconfig Tracer is a program for analysing the trace files generated by Bayesian MCMC runs (that is, the continuous parameter values sampled from the chain). It can be used to analyse runs of BEAST, MrBayes, LAMARC and possibly other MCMC programs.
  • Trim_Galore/0.6.5-GCCcore-8.3.0-Java-11-Python-3.7.4 Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data.
  • Trimmomatic/0.39-Java-11 Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line.
  • Trinity/2.8.4-foss-2018b easyconfig Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads.
  • UMI-tools/1.0.1-foss-2019b-Python-3.7.4 Tools for handling Unique Molecular Identifiers in NGS data sets
  • VCFtools/0.1.16-foss-2018b-Perl-5.28.0 easyconfig The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.
  • VSEARCH/2.9.1-foss-2018b VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads.
  • ViennaRNA/2.4.11-foss-2018b-Python-3.6.6 The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
  • ViennaRNA/2.4.11-foss-2018b-Python-3.6.6 The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures.
  • bam2fastx/1.3.0 easyconfig Conversion of PacBio BAM files into gzipped fasta and fastq files, including splitting of barcoded data
  • bam2wig/1.5 easyconfig Conversion of a BAM alignment to wiggle and bigwig coverage files, with flexible reporting options.
  • bcl2fastq2/2.20.0-foss-2019b easyconfig bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
  • bioawk/1.0-foss-2018b Bioawk is an extension to Brian Kernighan’s awk, adding the support of several common biological data formats, including optionally gzip’ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names.
  • biobambam2/2.0.95-foss-2018b easyconfig Tools for processing BAM files; bamsormadup, bamcollate2, bammarkduplicates, bammaskflags, bamrecompress, bamsort, bamtofastq
  • bx-python/0.8.8-foss-2019b-Python-3.7.4 easyconfig The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses.
  • cDNA_Cupcake/12.4.0-foss-2019b-Python-3.7.4 easyconfig cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data.
  • canu/1.8-foss-2018b-Perl-5.28.0 Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing
  • cas-offinder/2.4-foss-2018b easyconfig Cas-OFFinder is OpenCL based, ultrafast and versatile program that searches for potential off-target sites of CRISPR/Cas-derived RNA-guided endonucleases (RGEN).
  • cellranger/3.0.2-foss-2018b Chromium Single Cell Software Suite is a set of software applications for analyzing and visualizing single cell 3’ RNA-seq data produced by the 10x Genomics Chromium Platform.
  • cellranger-atac/1.1.0-foss-2018b The Chromium Single Cell ATAC Software Suite is a complete package for analyzing and visualizing single cell chromatin accessibility data produced by the Chromium Single Cell ATAC Solution on the 10x Chromium Platform.
  • cromwell/53-Java-1.8 easyconfig Scientific workflow engine designed for simplicity & scalability.
  • cutadapt/2.9-foss-2019b-Python-3.7.4 easyconfig Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.
  • deepTools/3.3.1-foss-2018b-Python-3.6.6 easyconfig deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq.
  • delly/0.8.3 easyconfig DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  • factera/1.4.4-foss-2018b-Perl-5.28.0 (Fusion And Chromosomal Translocation Enumeration and Recovery Algorithm) is a tool for detection of genomic fusions in paired-end targeted (or genome-wide) sequencing data.
  • fastq-tools/0.8-foss-2018b This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files.
  • gffread/0.11.6-GCCcore-8.3.0 GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
  • ggVennDiagram/3484e8-foss-2019b-R-4.0.2 easyconfig A set of functions to generate high-resolution Venn and Euler plots. Includes handling for several special cases, including two-case scaling, and extensive customization of plot shape and structure.
  • guidescan/1.2-foss-2018b-Python-2.7.15 easyconfig A generalized CRISPR guideRNA design tool.
  • hivmmer/0.1.2-foss-2018b-Python-3.6.6 easyconfig An alignment and variant-calling pipeline for Illumina deep sequencing of HIV-1, based on the probabilistic aligner HMMER
  • iCount/20180820-foss-2018b-Python-3.6.6 iCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions.
  • interop/1.1.10-foss-2019b-Python-3.7.4 easyconfig The Illumina InterOp libraries are a set of common routines used for reading InterOp metric files produced by Illumina sequencers including NextSeq 1k/2k. These libraries are backwards compatible and capable of supporting prior releases of the software, with one exception: GA systems have been excluded.
  • itpp/4.3.1-foss-2019b easyconfig IT++ is a C++ library of mathematical, signal processing and communication classes and functions. Its main use is in simulation of communication systems and for performing research in the area of communications.
  • kallisto/0.45.0-foss-2018b kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads.
  • king/2.2.5 easyconfig KING is a toolset that makes use of high-throughput SNP data typically seen in a genome-wide association study (GWAS) or a sequencing project. Applications of KING include family relationship inference and pedigree error checking, quality control, population substructure identification, forensics, gene mapping, etc.
  • libcerf/1.13-GCCcore-8.3.0 libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions.

  • libgtextutils/0.7-GCCcore-8.3.0 easyconfig ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream
  • libpll/0.3.2-GCCcore-7.3.0 easyconfig libpll is a versatile high-performance software library for phylogenetic analysis.
  • lumpy/0.2.13-foss-2018b easyconfig A probabilistic framework for structural variant discovery.
  • magicblast/1.5.0-gompi-2019b easyconfig Magic-BLAST is a new tool for mapping large sets of next-generation RNA or DNA sequencing runs against a whole genome or transcriptome.
  • manta/1.6.0 easyconfig Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.

  • minimap2/2.13-foss-2018b Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment.
  • monocle3/0.2.2-foss-2019b-R-4.0.2 easyconfig Single-cell transcriptome sequencing (sc-RNA-seq) experiments allow us to discover new cell types and help us understand how they arise in development. The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments.
  • nanofilt/2.5.0-foss-2018b-Python-3.6.6 easyconfig Filtering and trimming of long read sequencing data.
  • nanopolish/0.11.1-foss-2018b-Python-2.7.15 easyconfig Software package for signal-level analysis of Oxford Nanopore sequencing data.
  • ncbi-vdb/2.9.3-foss-2018b The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives.
  • ncdf4/1.17-foss-2019b ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files
  • nullarbor/2.0.20191013 easyconfig Pipeline to generate complete public health microbiology reports from sequenced isolates

  • numexpr/2.7.1-foss-2020a-Python-3.8.2 The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime.
  • oncosnpseq/2.01 easyconfig OncoSNP-SEQ is an analytical tool for characterising copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from whole genome sequencing data.
  • ont-guppy-cpu/2.3.7 Guppy is a production basecaller provided by Oxford Nanopore, and uses a command-line interface.
  • parasail/2.4-foss-2018b easyconfig parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms.
  • philosopher/3.2.9 easyconfig Philosopher provides easy access to third-party tools and custom algorithms allowing users to develop proteomics analysis, from Peptide Spectrum Matching to annotated protein reports. Philosopher is also tuned for Open Search analysis, providing a modified version of the prophets for peptide validation and protein inference. To this date, Philosopher is the only proteomics toolkit that allows you to process and analyze close and open search results.
  • picard/2.21.6-Java-11 A set of tools (in Java) for working with next generation sequencing data in the BAM format.
  • plink/1.9-20200616 easyconfig Whole-genome association analysis toolset
  • pplacer/1.1.alpha19-foss-2018b easyconfig Pplacer places reads on a phylogenetic tree. guppy (Grand Unified Phylogenetic Placement Yanalyzer) yanalyzes them. rppr is a helpful tool for working with reference packages.
  • prodigal/2.6.3-GCCcore-7.3.0 Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee.
  • prokka/1.14.5-gompi-2019b Prokka is a software tool for the rapid annotation of prokaryotic genomes.
  • psipred/4.02-foss-2018b easyconfig The PSIPRED Protein Sequence Analysis Workbench aggregates several UCL structure prediction methods into one location.
  • pyBigWig/0.3.17-foss-2019b-Python-3.7.4 easyconfig A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files.
  • pyGenomeTracks/3.5-foss-2019b-Python-3.7.4 easyconfig pyGenomeTracks aims to produce high-quality genome browser tracks that are highly customizable.
  • pybedtools/0.8.1-foss-2020a pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
  • python-parasail/1.1.16-foss-2018b-Python-3.6.6 This package contains Python bindings for parasail.
  • qcat/1.0.7-foss-2018b-Python-3.6.6 easyconfig Qcat is Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files.
  • samblaster/0.1.24-foss-2018b easyconfig samblaster is a fast and flexible program for marking duplicates in read-id grouped1 paired-end SAM files.
  • scanpy/1.4.6-foss-2019b-Python-3.7.4 easyconfig scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling.
  • seqtk/1.3-GCC-8.3.0 Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip.
  • seqtools/4.44.1-foss-2019b easyconfig The SeqTools package contains three tools for visualising sequence alignments: Blixem, Dotter and Belvu.
  • sequenza-utils/3.0.0-GCCcore-8.3.0-Python-3.7.4 Sequenza is a software for the estimation and quantification of purity/ploidy and copy number alteration in sequencing experiments of tumor samples. Sequenza-utils provide command lines programs to transform common NGS file format
  • smallgenomeutilities/0.2.1-foss-2018b-Python-3.6.6 easyconfig The smallgenomeutilities are a collection of scripts that is useful for dealing and manipulating NGS data of small viral genomes. They are written in Python 3 with a small number of dependencies.
  • snippy/4.6.0-foss-2019b-Perl-5.30.0 Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment.
  • strelka/2.9.9-foss-2018b Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs.
  • tabix/0.2.6-GCCcore-8.3.0 Generic indexer for TAB-delimited genome position files
  • terraphast/master-foss-2018b easyconfig libpll is a versatile high-performance software library for phylogenetic analysis.
  • vcflib/1.0.1-GCCcore-8.3.0 easyconfig vcflib provides methods to manipulate and interpret sequence variation as it can be described by VCF. The Variant Call Format (VCF) is a flat-file, tab-delimited textual format intended to concisely describe reference-indexed genetic variations between individuals.
  • velocyto.R/0.6-foss-2019b-R-4.0.2 easyconfig velocyto (velox + κύτος, quick cell) is a package for the analysis of expression dynamics in single cell RNA seq data. In particular, it enables estimations of RNA velocities of single cells by distinguishing unspliced and spliced mRNAs in standard single-cell RNA sequencing protocols (see pre-print below for more information).
  • vt/0.57721-foss-2019b easyconfig A tool set for short variant discovery in genetic sequence data.
  • wot/1.0.8-foss-2018b-Python-3.6.6 easyconfig Single-cell RNA sequencing is a powerful technology that can reveal a lot about what happens in a group of cells as they develop. But because the technology destroys a cell, it can only provide snapshots of the cells in a group at one point in time. To really understand how cells develop over time, snapshots aren’t good enough: scientists want to fill in the gaps between snapshots and string everything together into a movie.

Updated: September 17, 2020

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