All Modules 18.04

  • ATK/2.34.1-GCCcore-8.3.0 ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications.

  • 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.
  • Anaconda3/2020.02 Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture.

  • Arrow/0.15.1-foss-2018b-Python-3.6.6 easyconfig Apache Arrow (incl. PyArrow Python bindings)), a cross-language development platform for in-memory data.
  • Aspera-Connect/3.9.6 Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server.
  • Autoconf/2.69-GCCcore-9.3.0 Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls.

  • Automake/1.16.2-GCCcore-10.2.0 Automake: GNU Standards-compliant Makefile generator
  • Autotools/20200321-GCCcore-10.2.0 This bundle collect the standard GNU build tools: Autoconf, Automake and libtool

  • BBMap/38.79-GCC-8.3.0 BBMap short read aligner, and other bioinformatic tools.
  • BCFtools/1.9-GCC-8.3.0 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-10.2.0 easyconfig 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+/2.10.1-gompi-2020a 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-GCC-8.3.0 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-2018b easyconfig BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files.
  • Bazel/0.29.1-GCCcore-8.3.0 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google’s software.
  • 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/1.78-foss-2020b-Python-3.8.6 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.
  • Bison/3.7.1 Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables.

  • Blosc/1.18.1-foss-2019b easyconfig Blosc, an extremely fast, multi-threaded, meta-compressor library
  • Boost/1.72.0-gompi-2019b easyconfig Boost provides free peer-reviewed portable C++ source libraries.
  • Boost.Python/1.67.0-foss-2018b-Python-2.7.15 Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language.
  • Bowtie/1.2.3-GCC-8.3.0 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.
  • CARBayes/5.1.1-foss-2018b-R-3.5.2 easyconfig Implements a class of univariate and multivariate spatial generalised linear mixed models for areal unit data, with inference in a Bayesian setting using Markov chain Monte Carlo (MCMC) simulation.
  • 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.
  • CMake/3.18.4-GCCcore-10.2.0 CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software.

  • 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.
  • CRIU/3.13-foss-2019b-Python-3.7.4 easyconfig Checkpoint/Restore In Userspace (CRIU) is a Linux software which can freeze a running container (or an individual application) and checkpoint its state to disk. The data saved can be used to restore the application and run it exactly as it was during the time of the freeze. Using this functionality, application or container live migration, snapshots, remote debugging, and many other things are now possible.
  • CUDA/10.2.89-GCC-8.3.0 CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs.
  • CellRanger/5.0.0 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
  • Clang/6.0.1-GCC-7.3.0-2.30 C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library – use libstdc++ from GCC.
  • Clp/1.17.6-GCCcore-8.3.0 easyconfig Clp (Coin-or linear programming) is an open-source linear programming solver
  • ClustalW2/2.1-foss-2019b ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins.
  • 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.
  • Coreutils/8.32-GCCcore-8.3.0 easyconfig The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system.

  • Cufflinks/2.2.1-foss-2018b easyconfig Transcript assembly, differential expression, and differential regulation for RNA-Seq
  • DB/18.1.40-GCCcore-10.2.0 Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects.
  • DB_File/1.835-GCCcore-8.3.0 easyconfig Perl5 access to Berkeley DB version 1.x.
  • DBus/1.13.18-GCCcore-10.2.0 D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a “single instance” application or daemon, and to launch applications and daemons on demand when their services are needed.

  • DIAMOND/0.9.22-foss-2018b easyconfig Accelerated BLAST compatible local sequence aligner
  • Doxygen/1.8.20-GCCcore-10.2.0 Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D.

  • EIGENSOFT/7.2.1-foss-2019b The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes.
  • 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.
  • ESS/18.10.2 easyconfig Emacs Speaks Statistics (ESS) is an add-on package for emacs text editors such as GNU Emacs and XEmacs. It is designed to support editing of scripts and interaction with various statistical analysis programs such as R, S-Plus, SAS, Stata and OpenBUGS/JAGS.
  • EasyBuild/4.3.2 EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way.
  • Eigen/3.3.8-GCCcore-10.2.0 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms.
  • Emacs/26.3-GCCcore-8.3.0-ESS easyconfig GNU Emacs is an extensible, customizable text editor—and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing.
  • 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.
  • FFTW/3.3.8-gompic-2019b FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data.
  • FFmpeg/4.2.1-GCCcore-8.3.0 A complete, cross-platform solution to record, convert and stream audio and video.
  • FIt-SNE/1.1.0-gompi-2018b easyconfig t-distributed stochastic neighbor embedding (t-SNE) is widely used for visualizing single-cell RNA-sequencing (scRNA-seq) data, but it scales poorly to large datasets. We dramatically accelerate t-SNE, obviating the need for data downsampling, and hence allowing visualization of rare cell populations. Furthermore, we implement a heatmap-style visualization for scRNA-seq based on one-dimensional t-SNE for simultaneously visualizing the expression patterns of thousands of genes.
  • 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.

  • FLTK/1.3.5-GCC-8.3.0 FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation.
  • 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.
  • File-ReadBackwards/1.05-GCCcore-7.3.0-Perl-5.28.0 This Perl module reads a file backwards line by line.
  • FriBidi/1.0.5-GCCcore-7.3.0 easyconfig The Free Implementation of the Unicode Bidirectional Algorithm.

  • 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.
  • GCC/10.2.0 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,…).
  • GCCcore/10.2.0 The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,…).
  • 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
  • GDAL/3.0.2-foss-2019b-Python-3.7.4 GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing.
  • GEOS/3.8.0-GCC-8.3.0-Python-3.7.4 GEOS (Geometry Engine
  • GISTIC/2.0.23-GCCcore-8.3.0 easyconfig GISTIC is a tool to identify genes targeted by somatic copy-number alterations (SCNAs) that drive cancer growth. By separating SCNA profiles into underlying arm-level and focal alterations, GISTIC estimates the background rates for each category as well as defines the boundaries of SCNA regions.
  • GLIPH2/0.1 GLIPH 2 clusters TCRs that are predicted to bind the same MHC-restricted peptide antigen.
  • GLPK/4.65-GCCcore-7.3.0 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.
  • GLib/2.66.1-GCCcore-10.2.0 GLib is one of the base libraries of the GTK+ project
  • GLibmm/2.49.7-GCCcore-8.3.0 C++ bindings for Glib
  • 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-10.2.0 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers.

  • GMime/3.2.7-GCCcore-8.3.0 easyconfig The GMime package contains a set of utilities for parsing and creating messages using the Multipurpose Internet Mail Extension (MIME) as defined by the applicable RFCs.
  • GObject-Introspection/1.66.1-GCCcore-10.2.0 GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library.
  • 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.

  • GSL/2.6-GCC-8.3.0 The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting.
  • GST-plugins-base/1.16.2-GCC-8.3.0 GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
  • GStreamer/1.16.2-GCC-8.3.0 GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing.
  • GTK+/3.24.13-GCCcore-8.3.0 GTK+ is the primary library used to construct user interfaces in GNOME. It provides all the user interface controls, or widgets, used in a common graphical application. Its object-oriented API allows you to construct user interfaces without dealing with the low-level details of drawing and device interaction.

  • GTS/0.7.6-foss-2018b easyconfig GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles.
  • Gdk-Pixbuf/2.38.2-GCCcore-8.3.0 The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3.

  • 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.
  • Ghostscript/9.53.3-GCCcore-10.2.0 Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that.
  • Giotto/1.0.0-foss-2019b-R-4.0.2 easyconfig The Giotto package consists of two modules, Giotto Analyzer and Viewer, which provide tools to process, analyze and visualize single-cell spatial expression data.
  • GitPython/3.1.0-GCCcore-8.3.0-Python-3.7.4 GitPython is a python library used to interact with Git repositories
  • GlobusConnectPersonal/3.1.1 easyconfig Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine—campus server, desktop computer or laptop—even if it’s behind a firewall and you don’t have administrator privileges.

  • Go/1.14.1 Go is an open source programming language that makes it easy to build simple, reliable, and efficient software.
  • GraphicsMagick/1.3.31-foss-2018b easyconfig GraphicsMagick is the swiss army knife of image processing.
  • Graphviz/2.42.2-foss-2019b Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains.
  • HDF5/1.10.7-gompi-2020b HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data.
  • 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.
  • HOME/1.0.0-foss-2019b-Python-3.7.4 easyconfig HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification. The method uses histogram of methylation features and the linear Support Vector Machine (SVM) to identify DMRs from whole genome bisulfite sequencing (WGBS) data.
  • 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-PIC A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix
  • HarfBuzz/2.6.4-GCCcore-8.3.0 easyconfig HarfBuzz is an OpenType text shaping engine.
  • ICU/67.1-GCCcore-10.2.0 ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications.
  • 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.
  • IPython/7.15.0-foss-2020a-Python-3.8.2 IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing.
  • IgBLAST/1.15.0-x64-linux easyconfig IgBLAST faclilitates the analysis of immunoglobulin and T cell receptor variable domain sequences.
  • ImageMagick/7.0.10-35-GCCcore-10.2.0 ImageMagick is a software suite to create, edit, compose, or convert bitmap images
  • JAGS/4.3.0-foss-2020b easyconfig JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation
  • JUnit/4.12-Java-1.8 A programmer-oriented testing framework for Java.
  • JasPer/2.0.14-GCCcore-10.2.0 The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard.

  • Java/11.0.2 easyconfig The official Reference Implementation for Java SE 11 (JSR 384) is based solely upon open-source code available from the JDK 11 Project in the OpenJDK Community.
  • Jellyfish/2.2.10-foss-2018b Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
  • Judy/1.0.5-GCCcore-8.3.0 A C library that implements a dynamic array.
  • JupyterLab/2.2.5-foss-2020a-Python-3.8.2 JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook.
  • Kent_tools/20201201-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.
  • Kraken2/2.0.9-beta-gompi-2020a-Perl-5.30.2 Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm.
  • Krona/2.7.1-GCCcore-9.3.0-Perl-5.30.2 easyconfig Krona allows hierarchical data to be explored with zooming, multi-layered pie charts. Krona charts can be created using an Excel template or KronaTools, which includes support for several bioinformatics tools and raw data formats.
  • LAME/3.100-GCCcore-8.3.0 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL.
  • LAST/963-foss-2018b LAST finds similar regions between sequences.
  • LLVM/11.0.0-GCCcore-10.2.0 The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation (“LLVM IR”). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator.
  • LMDB/0.9.24-GCCcore-9.3.0 LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases.
  • LZO/2.10-foss-2018b easyconfig Portable lossless data compression library
  • LibSoup/2.70.0-GCCcore-8.3.0 libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications.
  • LibTIFF/4.1.0-GCCcore-10.2.0 tiff: Library and tools for reading and writing TIFF data files
  • LightGBM/2.2.3-foss-2018b easyconfig A fast, distributed, high performance gradient boosting (GBT, GBDT, GBRT, GBM or MART) framework based on decision tree algorithms, used for ranking, classification and many other machine learning tasks.
  • LittleCMS/2.11-GCCcore-10.2.0 Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance.
  • LoFreq/2.1.3.1-foss-2018b-Python-2.7.15 Fast and sensitive variant calling from next-gen sequencing data
  • Lua/5.1.5-GCCcore-8.3.0 Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping.
  • M4/1.4.18-GCCcore-10.2.0 GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc.
  • MACS2/2.2.6-foss-2019b-Python-3.7.4 Model Based Analysis for ChIP-Seq data
  • MAESTRO/1.2.1-foss-2019b-Python-3.7.4 easyconfig MAESTRO(Model-based AnalysEs of Single-cell Transcriptome and RegulOme) is a comprehensive single-cell RNA-seq and ATAC-seq analysis suit built using snakemake. MAESTRO combines several dozen tools and packages to create an integrative pipeline, which enables scRNA-seq and scATAC-seq analysis from raw sequencing data (fastq files) all the way through alignment, quality control, cell filtering, normalization, unsupervised clustering, differential expression and peak calling, celltype annotation and transcription regulation analysis.
  • 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.
  • MAGeCK-VISPR/0.5.5-Python-3.7.4 easyconfig MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens The workflow combines the MAGeCK algorithm to identify essential genes from CRISPR/Cas9 screens considering multiple conditions with VISPR to interactively explore results and quality control in a web-based frontend.
  • MAGeCK-VISPR/0.5.5-Python-3.7.4 MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens The workflow combines the MAGeCK algorithm to identify essential genes from CRISPR/Cas9 screens considering multiple conditions with VISPR to interactively explore results and quality control in a web-based frontend.
  • MAGeCK-VISPR/0.5.5-Python-3.7.4 MAGeCK-VISPR is a comprehensive quality control, analysis and visualization workflow for CRISPR/Cas9 screens The workflow combines the MAGeCK algorithm to identify essential genes from CRISPR/Cas9 screens considering multiple conditions with VISPR to interactively explore results and quality control in a web-based frontend.
  • MEME/5.1.1-foss-2019b-Perl-5.30.0-Python-3.7.4 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.
  • Mako/1.1.3-GCCcore-10.2.0 easyconfig A super-fast templating language that borrows the best ideas from the existing templating languages
  • MariaDB/10.5.1-foss-2019b easyconfig MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga.
  • MariaDB-connector-c/2.3.7-GCCcore-8.3.0 MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases.
  • MaxQuant/1.6.17.0-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.
  • Mesa/20.2.1-GCCcore-10.2.0 Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics.
  • Meson/0.55.3-GCCcore-10.2.0 Meson is a cross-platform build system designed to be both as fast and as user friendly as possible.
  • 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-9.3.0-Java-11 easyconfig Mining CRISPRs in Environmental Datasets
  • Miniconda3/4.7.10 easyconfig Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages.
  • Mono/6.8.0.105-GCCcore-8.3.0 An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET.
  • 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.
  • MutSigCV/1.3.4-pre.2 MutSigCV accepts whole genome or whole exome sequencing data from multiple samples, with information about point mutations, small insertions/deletions, and coverage, and identifies genes that are mutated more often than one would expect by chance.

  • NASM/2.15.05-GCCcore-10.2.0 NASM: General-purpose x86 assembler
  • 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.
  • NLopt/2.6.2-GCCcore-10.2.0 NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms.
  • NSPR/4.29-GCCcore-10.2.0 Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions.
  • NSS/3.57-GCCcore-10.2.0 Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications.
  • Nim/0.19.2-GCCcore-7.3.0 Nim is a systems and applications programming language.
  • Ninja/1.10.1-GCCcore-10.2.0 Ninja is a small build system with a focus on speed.
  • OpenBLAS/0.3.12-GCC-10.2.0 OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.
  • OpenJPEG/2.4.0-GCCcore-10.2.0 easyconfig OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software.
  • OpenMPI/4.0.5-GCC-10.2.0 The Open MPI Project is an open source MPI-3 implementation.
  • OpenPGM/5.2.122-GCCcore-9.3.0 OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility.

  • 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.
  • PCRE/8.44-GCCcore-9.3.0 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

  • PCRE2/10.35-GCCcore-10.2.0 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5.

  • 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
  • PMIx/3.1.5-GCCcore-10.2.0 Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions
  • PROJ/6.2.1-GCCcore-8.3.0 Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates
  • Pandoc/2.10 If you need to convert files from one markup format into another, pandoc is your swiss-army knife
  • Pango/1.44.7-GCCcore-8.3.0 easyconfig Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x.
  • Perl/5.32.0-GCCcore-10.2.0 Larry Wall’s Practical Extraction and Report Language
  • Pillow/8.0.1-GCCcore-10.2.0 Pillow is the ‘friendly PIL fork’ by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors.
  • 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
  • PostgreSQL/12.3-GCCcore-9.3.0-Python-3.8.2 PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation.
  • PyCairo/1.18.0-foss-2018b-Python-3.6.6 Python bindings for the cairo library
  • PyClone/2020.9b2-GCCcore-10.2.0 PyClone is a Python package that wraps rclone and provides a threaded interface for an installation at the host or container level.
  • PyQt5/5.11.3-foss-2018b-Python-3.6.6 PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company.
  • PyTables/3.6.1-foss-2020a-Python-3.8.2 PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases.
  • PyYAML/5.3.1-GCCcore-10.2.0 PyYAML is a YAML parser and emitter for the Python programming language.
  • 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-10.2.0 easyconfig 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.
  • Python/3.8.6-GCCcore-10.2.0 Python is a programming language that lets you work more quickly and integrate your systems more effectively.
  • Qt/4.8.7-foss-2018b Qt is a comprehensive cross-platform C++ application framework.
  • Qt5/5.14.2-GCCcore-10.2.0 Qt is a comprehensive cross-platform C++ application framework.
  • R/4.0.3-foss-2020b easyconfig R is a free software environment for statistical computing and graphics.
  • 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’.
  • RELION/3.1.0-foss-2019b easyconfig RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy.
  • 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.
  • Racon/1.4.13-GCCcore-8.3.0 Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads.
  • 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.
  • Ruby/2.7.1-GCCcore-8.3.0 Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write.
  • Rust/1.42.0-GCCcore-8.3.0 easyconfig Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety.
  • 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.
  • SCons/3.1.1-GCCcore-8.3.0 SCons is a software construction tool.
  • SDL2/2.0.10-GCCcore-8.3.0 SDL: Simple DirectMedia Layer, a cross-platform multimedia library
  • 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.
  • SQLite/3.33.0-GCCcore-10.2.0 SQLite: SQL Database Engine in a C Library
  • 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/2.7.6a-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.
  • SVG/2.84-foss-2019b-Perl-5.30.0 Perl binding for SVG
  • SWIG/4.0.1-GCCcore-8.3.0 SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages.
  • SYMPHONY/5.6.17-GCCcore-8.3.0 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.
  • ScaLAPACK/2.1.0-gompi-2020b The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers.
  • SciPy-bundle/2020.11-foss-2020b Bundle of Python packages for scientific software
  • 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.
  • Singularity/3.5.3 Singularity is a portable application stack packaging and runtime utility.
  • 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.
  • Sphinx/1.8.1-foss-2018b-Python-3.6.6 Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well.
  • 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.

  • Subread/2.0.0-GCC-8.3.0 High performance read alignment, quantification and mutation discovery
  • Szip/2.1.1-GCCcore-9.3.0 Szip compression software, providing lossless compression of scientific data

  • TRF/4.09-linux64 Tandem repeats finder: a program to analyze DNA sequences. Legacy version.
  • Tcl/8.6.10-GCCcore-9.3.0 Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more.

  • TensorFlow/2.1.0-foss-2019b-Python-3.7.4 easyconfig An open-source software library for Machine Intelligence
  • 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.
  • Tk/8.6.10-GCCcore-10.2.0 Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages.
  • Tkinter/3.8.6-GCCcore-10.2.0 Tkinter module, built with the Python buildsystem
  • 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.
  • UCX/1.9.0-GCCcore-10.2.0 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications

  • UDUNITS/2.2.26-foss-2018b UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement.
  • UMI-tools/1.0.1-foss-2019b-Python-3.7.4 Tools for handling Unique Molecular Identifiers in NGS data sets
  • UnZip/6.0-GCCcore-7.3.0 UnZip is an extraction utility for archives compressed in .zip format (also called “zipfiles”). Although highly compatible both with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s own Zip program, our primary objectives have been portability and non-MSDOS functionality.
  • 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.
  • VTK/8.2.0-foss-2019b-Python-3.7.4 The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation.
  • 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.
  • WebKitGTK+/2.27.4-GCC-8.3.0 WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit’s full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions.
  • WiggleTools/1.2.4-GCC-8.3.0 easyconfig The WiggleTools package allows genomewide data files to be manipulated as numerical functions, equipped with all the standard functional analysis operators (sum, product, product by a scalar, comparators), and derived statistics (mean, median, variance, stddev, t-test, Wilcoxon’s rank sum test, etc).
  • X11/20201008-GCCcore-10.2.0 The X Window System (X11) is a windowing system for bitmap displays
  • XGBoost/0.90-foss-2019b-Python-3.7.4 XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable.
  • XML-LibXML/2.0201-GCCcore-8.3.0 Perl binding for libxml2
  • XML-Parser/2.44_01-GCCcore-7.3.0-Perl-5.28.0 This is a Perl extension interface to James Clark’s XML parser, expat.
  • XZ/5.2.5-GCCcore-9.3.0 xz: XZ utilities
  • Xerces-C++/3.2.0-GCCcore-7.3.0 Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs.
  • Xvfb/1.20.9-GCCcore-10.2.0 Xvfb is an X server that can run on machines with no display hardware and no physical input devices. It emulates a dumb framebuffer using virtual memory.
  • Yasm/1.3.0-GCCcore-8.3.0 Yasm: Complete rewrite of the NASM assembler with BSD license
  • ZeroMQ/4.3.3-GCCcore-10.2.0 ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It’s fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems.
  • Zip/3.0-GCCcore-8.3.0 Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s own UnZip, our primary objectives have been portability and other-than-MSDOS functionality
  • agrep/2.04-GCCcore-8.3.0 easyconfig AGREP
  • ancestry/1.0.0-GCCcore-8.3.0-Python-2.7.16 easyconfig Fast individual ancestry inference from DNA sequence data leveraging allele frequencies from multiple populations. iAdmix Using population allele frequencies for computing individual admixture estimates
  • ancestry/1.0.0-GCCcore-8.3.0-Python-2.7.16 Fast individual ancestry inference from DNA sequence data leveraging allele frequencies from multiple populations. iAdmix Using population allele frequencies for computing individual admixture estimates
  • ant/1.10.6-Java-1.8 Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications.
  • arcasHLA/0.2.0-foss-2019b-Python-3.7.4 arcasHLA performs high resolution genotyping for HLA class I and class II genes from RNA sequencing, supporting both paired and single-end samples.
  • at-spi2-atk/2.34.1-GCCcore-8.3.0 AT-SPI 2 toolkit bridge

  • at-spi2-core/2.34.0-GCCcore-8.3.0 Assistive Technology Service Provider Interface.

  • awscli/2.0.55-GCCcore-9.3.0-Python-3.8.2 Universal Command Line Environment for AWS
  • 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.
  • basicfiltering/1.0.7-foss-2020a-Python-3.8.2 easyconfig Basic Filtering for; Variant Allele Frequency, Variat Reads, tumor-Normal Variant Allele Frequencey Ratio.
  • bcl2fastq/1.8.4 easyconfig

  • bcl2fastq2/2.20.0-foss-2018b bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis.
  • beagle-lib/3.1.2-GCCcore-8.3.0 beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages.
  • binutils/2.35 binutils: GNU binary utilities
  • 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
  • bokeh/2.0.2-foss-2020a-Python-3.8.2 Statistical and novel interactive HTML plots for Python
  • brotli/1.0.9-GCC-8.3.0 Brotli is a generic-purpose lossless compression algorithm that compresses data using a combination of a modern variant of the LZ77 algorithm, Huffman coding and 2nd order context modeling, with a compression ratio comparable to the best currently available general-purpose compression methods. It is similar in speed with deflate but offers more dense compression.

The specification of the Brotli Compressed Data Format is defined in RFC 7932.

  • bsddb3/6.2.7-foss-2019b-Python-2.7.16 easyconfig bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects.
  • 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.
  • bzip2/1.0.8-GCCcore-10.2.0 bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression.

  • 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.
  • cURL/7.72.0-GCCcore-10.2.0 libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more.

  • cairo/1.16.0-GCCcore-10.2.0 Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB
  • canu/1.8-foss-2018b easyconfig 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).
  • ccache/3.7.9-GCCcore-8.3.0 easyconfig Cache for C/C++ compilers
  • 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.
  • cisTEM/1.0.0-beta cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them.
  • cromwell/54-Java-1.8 easyconfig Scientific workflow engine designed for simplicity & scalability.
  • ctffind/4.1.14-fosscuda-2019b Program for finding CTFs of electron micrographs.
  • cupcake/0.0.4-foss-2019b-Python-3.7.4 easyconfig Cupcake is a thin layer over CMake and Conan that tries to offer a better user experience in the style of Yarn or Poetry.
  • 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.
  • dask/2.18.1-foss-2020a-Python-3.8.2 Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love.
  • deepTools/3.3.1-foss-2019b-Python-3.7.4 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
  • double-conversion/3.1.5-GCCcore-9.3.0 Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles.
  • edlib/1.3.8.post1-GCC-8.3.0-Python-3.7.4 Lightweight, super fast library for sequence alignment using edit (Levenshtein) distance.
  • expat/2.2.9-GCCcore-10.2.0 Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags)

  • expect/5.45.4-GCCcore-9.3.0 easyconfig Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications.
  • factera/1.4.4-foss-2019b-Perl-5.30.0 easyconfig (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.
  • fast5/0.6.5 easyconfig A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data.
  • fastp/0.20.0-GCC-8.3.0 A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance.
  • 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.
  • fhDev/GCCcore-8.3.0 fhDev Fred Hutch Development environment is a collection of development tools that will work with LMOD modules for a given environment.

  • fhPython/3.8.2-foss-2020a-Python-3.8.2 Fred Hutch Python
  • fhR/4.0.3-foss-2020b R is a free software environment for statistical computing and graphics.
  • fig2dev/3.2.6a-foss-2019b Xfig is an interactive drawing tool which runs under X Window System.
  • file/5.38-GCCcore-8.3.0 The file command is ‘a file type guesser’, that is, a command-line tool that tells you in words what kind of data a file contains.
  • flex/2.6.4-GCCcore-9.3.0 Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text.

  • fontconfig/2.13.92-GCCcore-9.3.0 Fontconfig is a library designed to provide system-wide font configuration, customization and application access.

  • foss/2020b GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
  • fosscuda/2019b GCC based compiler toolchain with CUDA support, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK.
  • freebayes/1.3.2-GCCcore-8.3.0 Bayesian haplotype-based polymorphism discovery and genotyping.
  • freeglut/3.2.1-GCCcore-8.3.0 freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library.
  • freetds/1.2-GCCcore-9.3.0 easyconfig FreeTDS is a set of libraries for Unix and Linux that allows your programs to natively talk to Microsoft SQL Server and Sybase databases.
  • freetype/2.10.3-GCCcore-10.2.0 FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well.

  • future/0.16.0-foss-2019b-Python-3.7.4 easyconfig python-future is the missing compatibility layer between Python 2 and Python 3.
  • g2lib/3.1.0-foss-2018b Library contains GRIB2 encoder/decoder and search/indexing routines.
  • gc/7.6.4-GCCcore-7.3.0 The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new.

  • gcccuda/2019b GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit.
  • gdc-client/1.5.0-foss-2019b-Python-3.7.4 The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS.
  • gettext/0.21-GCCcore-10.2.0 GNU ‘gettext’ is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation
  • gffread/0.11.6-GCCcore-8.3.0 GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more.
  • gflags/2.2.2-GCCcore-8.3.0 The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used.

  • 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.
  • gh/1.3.1 easyconfig gh is GitHub on the command line.
  • giflib/5.2.1-GCCcore-8.3.0 giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented.
  • git/2.23.0-GCCcore-8.3.0-nodocs Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency.
  • git-lfs/2.11.0 easyconfig Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com
  • glew/2.1.0-GCCcore-8.3.0 The OpenGL Extension Wrangler Library

The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. OpenGL core and extension functionality is exposed in a single header file. GLEW has been tested on a variety of operating systems, including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris.

  • glog/0.4.0-GCCcore-8.3.0 A C++ implementation of the Google logging module.
  • gnuplot/5.2.8-GCCcore-8.3.0 Portable interactive, function plotting utility
  • gompi/2020b GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support.
  • gompic/2019b GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled.
  • gperf/3.1-GCCcore-8.3.0 easyconfig GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only.

  • graphite2/1.3.14-GCCcore-8.3.0 easyconfig Graphite is a “smart font” system developed specifically to handle the complexities of lesser-known languages of the world.
  • gsutil/4.50-GCCcore-8.3.0-Python-3.7.4 easyconfig gsutil is a Python application that lets you access Cloud Storage from the command line.
  • gtest/1.8.1-GCCcore-8.3.0 Google’s framework for writing C++ tests on a variety of platforms
  • guidescan/1.2-foss-2018b-Python-2.7.15 easyconfig A generalized CRISPR guideRNA design tool.
  • gzip/1.10-GCCcore-10.2.0 gzip (GNU zip) is a popular data compression program as a replacement for compress
  • h5py/2.10.0-foss-2018b-Python-3.6.6 easyconfig HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data.
  • help2man/1.47.16-GCCcore-10.2.0 help2man produces simple manual pages from the ‘–help’ and ‘–version’ output of other commands.
  • 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
  • hwloc/2.2.0-GCCcore-10.2.0 The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, …) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently.

  • hypothesis/5.41.2-GCCcore-10.2.0 Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work.
  • 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.
  • igraph/0.8.2-foss-2020a easyconfig igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++.
  • index-hopping-filter/1.0.1 index-hopping-filter is a tool that filters index hopped reads from a set of demultiplexed samples. The tool detects and removes likely index hopped reads from demultiplexed FASTQs, and in turn emits new, filtered, FASTQs with similar file and directory layout as the inputs, suitable for use with cellranger count and cellranger vdj.
  • 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.
  • intervene/0.6.4-foss-2019b-Python-3.7.4 easyconfig Intervene a tool for intersection and visualization of multiple genomic region sets
  • intltool/0.51.0-GCCcore-10.2.0 intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.
  • 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.
  • jbigkit/2.1-GCCcore-8.3.0 easyconfig JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents.
  • jemalloc/5.2.1-GCCcore-8.3.0 jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support.
  • kallisto/0.46.1-foss-2019b 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.
  • lftp/4.9.1-GCCcore-8.3.0 LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind.
  • libBigWig/0.4.4-GCCcore-8.3.0 A C library for handling bigWig files
  • libGLU/9.0.1-GCCcore-10.2.0 The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL.
  • libXaw3d/1.6.3-GCCcore-8.3.0 X11 client-side library
  • libaio/0.3.111-GCCcore-8.3.0 easyconfig Asynchronous input/output library that uses the kernels native interface.
  • libarchive/3.4.3-GCCcore-10.2.0 Multi-format archive and compression library

  • libasound/1.2.2-GCCcore-8.3.0 easyconfig The libnl suite is a collection of libraries providing APIs to netlink protocol based Linux kernel interfaces.
  • 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.

  • libcroco/0.6.13-GCCcore-8.3.0 easyconfig Libcroco is a standalone css2 parsing and manipulation library.
  • libdrm/2.4.102-GCCcore-10.2.0 Direct Rendering Manager runtime library.
  • libedit/20191231-GCC-8.3.0 This BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline.
  • libepoxy/1.5.4-GCCcore-8.3.0 Epoxy is a library for handling OpenGL function pointer management for you
  • libevent/2.1.12-GCCcore-10.2.0 The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts.

  • libfabric/1.11.0-GCCcore-10.2.0 Libfabric is a core component of OFI. It is the library that defines and exports the user-space API of OFI, and is typically the only software that applications deal with directly. It works in conjunction with provider libraries, which are often integrated directly into libfabric.

  • libffi/3.3-GCCcore-9.3.0 The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time.
  • libgcrypt/1.8.5-GCCcore-8.3.0 Libgpg-error is a small library that defines common error values for all GnuPG components.
  • libgd/2.2.5-GCCcore-8.3.0 GD is an open source code library for the dynamic creation of images by programmers.
  • libgeotiff/1.5.1-GCCcore-8.3.0 Library for reading and writing coordinate system information from/to GeoTIFF files
  • libgit2/1.1.0-GCCcore-10.2.0 easyconfig libgit2 is a portable, pure C implementation of the Git core methods provided as a re-entrant linkable library with a solid API, allowing you to write native speed custom Git applications in any language which supports C bindings.
  • libglvnd/1.3.2-GCCcore-10.2.0 libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors.
  • libgpg-error/1.38-GCCcore-8.3.0 Libgpg-error is a small library that defines common error values for all GnuPG components.
  • libgtextutils/0.7-GCCcore-8.3.0 easyconfig ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream
  • libharu/2.3.0-GCCcore-7.3.0 easyconfig libHaru is a free, cross platform, open source library for generating PDF files.
  • libiconv/1.16-GCCcore-10.2.0 Libiconv converts from one character encoding to another through Unicode conversion
  • libidn/1.35-GCCcore-9.3.0 GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn’s purpose is to encode and decode internationalized domain names.
  • libjpeg-turbo/2.0.5-GCCcore-10.2.0 libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding.

  • libmaus2/2.0.611-foss-2018b easyconfig libmaus2 is a collection of data structures and algorithms.
  • libpciaccess/0.16-GCCcore-10.2.0 Generic PCI access library.
  • libpll/0.3.2-GCCcore-7.3.0 easyconfig libpll is a versatile high-performance software library for phylogenetic analysis.
  • libpng/1.6.37-GCCcore-9.3.0 libpng is the official PNG reference library
  • libpsl/0.21.0-GCCcore-8.3.0 C library for the Public Suffix List
  • libpthread-stubs/0.4-GCCcore-8.3.0 The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility.

  • libreadline/8.0-GCCcore-8.3.0 The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands.

  • librsvg/2.49.1-foss-2019b librsvg is a library to render SVG files using cairo.
  • libsigc++/2.10.2-GCCcore-8.3.0 The libsigc++ package implements a typesafe callback system for standard C++.
  • libsndfile/1.0.28-GCCcore-10.2.0 Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface.
  • libsodium/1.0.18-GCCcore-8.3.0 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more.

  • libtasn1/4.16.0-GCCcore-8.3.0 Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package.
  • libtool/2.4.6-GCCcore-7.3.0 GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface.

  • libunistring/0.9.10-GCCcore-7.3.0 easyconfig This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard.

  • libunwind/1.4.0-GCCcore-10.2.0 The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications
  • libwebp/1.1.0-GCCcore-8.3.0 WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster.
  • libxml++/2.40.1-GCCcore-8.3.0 libxml++ is a C++ wrapper for the libxml XML parser library.
  • libxml2/2.9.10-GCCcore-9.3.0 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform).

  • libxslt/1.1.34-GCCcore-8.3.0 Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform).
  • libyaml/0.2.5-GCCcore-10.2.0 LibYAML is a YAML parser and emitter written in C.
  • lumpy/0.2.13-foss-2018b easyconfig A probabilistic framework for structural variant discovery.
  • lz4/1.9.2-GCCcore-10.2.0 LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core.
  • 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.

  • matplotlib/3.3.3-foss-2020b matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits.
  • minimap2/2.17-GCC-8.3.0 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.
  • monolix/2019R2 Monolix performs non-linear mixed effects modeling (NLME) for pharmacometrics.
  • 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
  • ncdu/1.15.1-GCCcore-8.3.0 Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don’t have an entire graphical setup available, but it is a useful tool even on regular desktop systems.
  • ncurses/6.2 The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses.
  • netCDF/4.7.4-gompi-2020a NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data.
  • nettle/3.6-GCCcore-10.2.0 Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, …), in applications like LSH or GNUPG, or even in kernel space.
  • networkx/2.4-foss-2019b-Python-3.7.4 NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
  • nextflow/20.09.0-edge Nextflow is a bioinformatics workflow manager that enables the development of portable and reproducible workflows. It supports deploying workflows on a variety of execution platforms including local, HPC schedulers, AWS Batch, Google Genomics Pipelines, and Kubernetes.
  • nodejs/12.19.0-GCCcore-10.2.0 Node.js is a platform built on Chrome’s JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices.
  • nullarbor/2.0.20191013 easyconfig Pipeline to generate complete public health microbiology reports from sequenced isolates

  • numactl/2.0.13-GCCcore-9.3.0 The numactl program allows you to run your application program on specific cpu’s and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program.

  • numba/0.50.0-foss-2020a-Python-3.8.2 Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code.
  • 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.
  • parallel/20200422-GCCcore-8.3.0 parallel: Build and execute shell commands in parallel
  • 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.
  • pbcopper/1.3.0-foss-2019b easyconfig The pbcopper library provides a suite of data structures, algorithms, and utilities for C++ applications.
  • philosopher/3.3.11 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.
  • pigz/2.4-GCCcore-8.3.0 pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries.

  • pipdeptree/0.13.2-foss-2019b-Python-3.7.4 easyconfig pipdeptree is a command line utility for displaying the installed python packages in form of a dependency tree. It works for packages installed globally on a machine as well as in a virtualenv.
  • pixman/0.40.0-GCCcore-10.2.0 Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server.

  • pkg-config/0.29.2-GCCcore-10.2.0 pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c pkg-config --libs --cflags glib-2.0 for instance, rather than hard-coding values on where to find glib (or other libraries).

  • pkgconfig/1.5.1-GCCcore-9.3.0-Python-3.8.2 pkgconfig is a Python module to interface with the pkg-config command line tool
  • plink/1.9-20200616 easyconfig Whole-genome association analysis toolset
  • plotly.py/4.4.1-foss-2019b An open-source, interactive graphing library for Python
  • pocl/1.2-GCC-7.3.0-2.30 easyconfig Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard
  • poetry/1.0.9-GCCcore-9.3.0-Python-3.8.2 easyconfig Python packaging and dependency management made easy
  • poppler/20.12.1-foss-2020b Poppler is a PDF rendering library based on the xpdf-3.0 code base.
  • popscle/0.1-beta-foss-2019b A suite of population scale analysis tools for single-cell genomics data including implementation of Demuxlet / Freemuxlet methods and auxilary tools
  • 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.
  • protobuf/3.10.0-GCCcore-8.3.0 easyconfig Google Protocol Buffers
  • protobuf-c/1.3.3-GCCcore-8.3.0 easyconfig This is protobuf-c, a C implementation of the Google Protocol Buffers data serialization format
  • 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-GCC-10.2.0 easyconfig pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python.
  • pybind11/2.6.0-GCCcore-10.2.0 pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code.
  • pyclone/0.13.1-foss-2019b-Python-2.7.16 PyClone is a Bayesian clustering method for grouping sets of deeply sequenced somatic mutations into putative clonal clusters while estimating their cellular prevalences and accounting for allelic imbalances introduced by segmental copy-number changes and normal-cell contamination.
  • pyspoa/0.0.4-GCC-8.3.0-Python-3.7.4 Python bindings to spoa.
  • pytest/5.4.1-foss-2019b-Python-3.7.4 pytest: simple powerful testing with Python
  • python-igraph/0.7.1.post6-foss-2018b-Python-3.6.6 Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.
  • 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.
  • re2c/2.0.3-GCCcore-10.2.0 re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons.
  • revbayes/1.0.11-foss-2018b RevBayes provides an interactive environment for statistical computation in phylogenetics. It is primarily intended for modeling, simulation, and Bayesian inference in evolutionary biology, particularly phylogenetics.
  • rgdal/1.4-8-foss-2019b-R-4.0.2 Provides bindings to the ‘Geospatial’ Data Abstraction Library (‘GDAL’) (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the ‘PROJ.4’ library.
  • rstudio/1.3.1093-foss-2019b-Java-11-R-4.0.2 easyconfig This RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R.

  • rstudio-server/1.2.5033-foss-2019b RStudio is an integrated development environment (IDE) for the R programming language.
  • 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.
  • scikit-learn/0.23.1-foss-2020a-Python-3.8.2 Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts.
  • seq2HLA/2.3-foss-2019b-Python-2.7.16 easyconfig In-silico method written in Python and R to determine HLA genotypes of a sample. seq2HLA takes standard RNA-Seq sequence reads in fastq format as input, uses a bowtie index comprising all HLA alleles and outputs the most likely HLA class I and class II genotypes (in 4 digit resolution), a p-value for each call, and the expression of each class.
  • 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.
  • snakemake/5.19.2-foss-2019b-Python-3.7.4 easyconfig The Snakemake workflow management system is a tool to create reproducible and scalable data analyses.
  • snappy/1.1.8-GCCcore-10.2.0 Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression.
  • 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.
  • spoa/4.0.0-GCC-8.3.0 Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences
  • stack/2.3.1

  • statsmodels/0.11.0-foss-2019b-Python-3.7.4 Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests.
  • 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-7.3.0 easyconfig Generic indexer for TAB-delimited genome position files
  • tagdust/2.33-GCCcore-8.3.0 easyconfig Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines.
  • tagdust/2.33-GCCcore-8.3.0 Raw sequences produced by next generation sequencing (NGS) machines may contain adapter, linker, barcode and fingerprint sequences. TagDust2 is a program to extract and correctly label the sequences to be mapped in downstream pipelines.
  • tcsh/6.20.00-GCCcore-7.3.0 Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax.
  • terminator/1.91-GCCcore-8.3.0-Python-2.7.16 Multiple terminals in one window. The goal of this project is to produce a useful tool for arranging terminals.
  • terraphast/master-foss-2018b easyconfig libpll is a versatile high-performance software library for phylogenetic analysis.
  • texinfo/6.7-GCCcore-8.3.0 Texinfo is the official documentation format of the GNU project.
  • texlive/20200624 TeX is a typesetting language. Instead of visually formatting your text, you enter your manuscript text intertwined with TeX commands in a plain text file. You then run TeX to produce formatted output, such as a PDF file. Thus, in contrast to standard word processors, your document is a separate file that does not pretend to be a representation of the final typeset output, and so can be easily edited and manipulated.
  • thrift/0.13.0-foss-2018b Thrift is a lightweight, language-independent software stack for point-to-point RPC implementation. Thrift provides clean abstractions and implementations for data transport, data serialization, and application level processing.
  • tmux/3.0-GCCcore-8.3.0 easyconfig tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal.
  • tqdm/4.47.0-GCCcore-9.3.0 A fast, extensible progress bar for Python and CLI
  • unixODBC/2.3.7-GCCcore-8.3.0 easyconfig unixODBC provides a uniform interface between application and database driver
  • util-linux/2.36-GCCcore-10.2.0 Set of Linux utilities
  • 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.
  • wget/1.20.3-GCCcore-9.3.0 GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc.
  • wheel/0.31.1-foss-2018b-Python-3.6.6 A built-package format for Python.
  • 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.
  • wxWidgets/3.1.3-GCC-8.3.0 wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform’s native API rather than emulating the GUI.
  • x264/20190925-GCCcore-8.3.0 x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL.

  • x265/3.2-GCCcore-8.3.0 x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL.

  • xbitmaps/1.1.2 provides bitmaps for x
  • xfig/3.2.6a-foss-2019b Xfig is an interactive drawing tool which runs under X Window System.
  • xorg-macros/1.19.2-GCCcore-9.3.0 X.org macros utilities.
  • xprop/1.2.4-GCCcore-8.3.0 The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information.
  • xproto/7.0.31-GCCcore-7.3.0 X protocol and ancillary headers
  • zlib/1.2.11-GCCcore-10.2.0 zlib is designed to be a free, general-purpose, legally unencumbered – that is, not covered by any patents – lossless data-compression library for use on virtually any computer hardware and operating system.
  • zstd/1.4.5-GCCcore-10.2.0 Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set.