-------------------------------------------------------------------------------------------------------------------------------- The following is a list of the modules and extensions currently available: -------------------------------------------------------------------------------------------------------------------------------- ABAQUS: ABAQUS/2022-hotfix-2223 Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. ABySS: ABySS/2.2.5 Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler ACTC: ACTC/1.1 ACTC converts independent triangles into triangle strips or fans. ADMIXTURE: ADMIXTURE/1.3.0 ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. AFNI: AFNI/23.1.07 AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. ANSYS: ANSYS/2023R1 ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. ANTLR: ANTLR/2.7.7-Java-11 ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. ANTs: ANTs/2.4.4 ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. APR: APR/1.7.0 Apache Portable Runtime (APR) libraries. APR-util: APR-util/1.6.1 Apache Portable Runtime (APR) util libraries. ARAGORN: ARAGORN/1.2.41 a program to detect tRNA genes and tmRNA genes in nucleotide sequences ATK: ATK/2.38.0 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. ATLAS: ATLAS/3.10.2-LAPACK-3.10.1 ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. AUGUSTUS: AUGUSTUS/3.5.0 AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences AmberTools: AmberTools/22.3 AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. Anaconda3: Anaconda3/2022.10 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. Apptainer: Apptainer/1.1.8 Apptainer is a portable application stack packaging and runtime utility. It replaces Singularity Archive-Zip: Archive-Zip/1.68 Provide an interface to ZIP archive files. Arrow: Arrow/8.0.0 Apache Arrow (incl. PyArrow Python bindings), a cross-language development platform for in-memory data. Autoconf: Autoconf/2.71 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: Automake/1.16.4, Automake/1.16.5 Automake: GNU Standards-compliant Makefile generator Autotools: Autotools/20220317 This bundle collect the standard GNU build tools: Autoconf, Automake and libtool BAMM: BAMM/2.5.0 BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. BBMap: BBMap/39.01 BBMap short read aligner, and other bioinformatic tools. BCFtools: BCFtools/1.15.1 Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants BEDTools: BEDTools/2.30.0 BEDTools: a powerful toolset for genome arithmetic. The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. BLAST: BLAST/2.14.0-Linux_x86_64 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. BLAST+: BLAST+/2.13.0 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: BLAT/3.7 BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. BLIS: BLIS/0.9.0 BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. BUSCO: BUSCO/5.4.5 BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs BWA: BWA/0.7.17 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: BamTools/2.5.2 BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. Bazel: Bazel/5.1.1 Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. Beast: Beast/1.10.4-CUDA-11.7.0, Beast/2.7.3-CUDA-11.7.0, Beast/2.7.3 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. BeautifulSoup: BeautifulSoup/4.10.0 Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. Bio-DB-HTS: Bio-DB-HTS/3.01 Read files using HTSlib including BAM/CRAM, Tabix and BCF database files Bio-SearchIO-hmmer: Bio-SearchIO-hmmer/1.7.3 Code to parse output from hmmsearch, hmmscan, phmmer and nhmmer, compatible with both version 2 and version 3 of the HMMER package from http://hmmer.org. BioPerl: BioPerl/1.7.8 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: Biopython/1.79 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. Bismark: Bismark/0.24.0 A tool to map bisulfite converted sequence reads and determine cytosine methylation states Bison: Bison/3.8.2 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: Blosc/1.21.3 Blosc, an extremely fast, multi-threaded, meta-compressor library Boost: Boost/1.79.0 Boost provides free peer-reviewed portable C++ source libraries. Boost.Python: Boost.Python/1.79.0 Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. Bottleneck: Bottleneck/1.3.7 Fast NumPy array functions written in C Bowtie: Bowtie/1.3.1 Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. Bowtie2: Bowtie2/2.4.5 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. Bracken: Bracken/2.7 Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample. Braken uses the taxonomy labels assigned by Kraken, a highly accurate metagenomics classification algorithm, to estimate the number of reads originating from each species present in a sample. Kraken classifies reads to the best matching location in the taxonomic tree, but does not estimate abundances of species. We use the Kraken database itself to derive probabilities that describe how much sequence from each genome is identical to other genomes in the database, and combine this information with the assignments for a particular sample to estimate abundance at the species level, the genus level, or above. Combined with the Kraken classifier, Bracken produces accurate species- and genus-level abundance estimates even when a sample contains two or more near-identical species. NOTE: Bracken is compatible with both Kraken 1 and Kraken 2. However, the default kmer length is different depending on the version of Kraken used. If you use Kraken 1 defaults, specify 31 as the kmer length. If you use Kraken 2 defaults, specify 35 as the kmer length. Brotli: Brotli/1.0.9 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. CAT: CAT/5.2.3 CAT/BAT: tool for taxonomic classification of contigs and metagenome-assembled genomes (MAGs) CD-HIT: CD-HIT/4.8.1 CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. CDO: CDO/2.2.0 CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. CFITSIO: CFITSIO/4.2.0 CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. CGAL: CGAL/4.14.3 The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. CLISP: CLISP/2.49 Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. CMake: CMake/3.12.1, CMake/3.23.1, CMake/3.24.3 CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. CNVnator: CNVnator/0.3.3 a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads COMSOL: COMSOL/5.6, COMSOL/6.0 COMSOL Multiphysics is a general-purpose software platform, based on advanced numerical methods, for modeling and simulating physics-based problems. CPLEX: CPLEX/22.1.1 IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability. CPMD: CPMD/4.3 The CPMD code is a parallelized plane wave / pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics. CUDA: CUDA/11.5.2, CUDA/11.7.0, CUDA/12.2.0 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. CapnProto: CapnProto/0.10.2 Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. CellRanger: CellRanger/7.0.0 Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. Centrifuge: Centrifuge/1.0.4 Classifier for metagenomic sequences Cereal: Cereal/1.3.0 cereal is a header-only C++11 serialization library. cereal takes arbitrary data types and reversibly turns them into different representations, such as compact binary encodings, XML, or JSON. cereal was designed to be fast, light-weight, and easy to extend - it has no external dependencies and can be easily bundled with other code or used standalone. CharLS: CharLS/2.4.1 CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios. Check: Check/0.15.2 Check is a unit testing framework for C. It features a simple interface for defining unit tests, putting little in the way of the developer. Tests are run in a separate address space, so both assertion failures and code errors that cause segmentation faults or other signals can be caught. Test results are reportable in the following: Subunit, TAP, XML, and a generic logging format. Circos: Circos/0.69-9 Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. Clang: Clang/12.0.1, Clang/13.0.1 C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. CloudCompare: CloudCompare/2.12.4 3D point cloud and mesh processing software Clustal-Omega: Clustal-Omega/1.2.4 Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms Compress-Raw-Zlib: Compress-Raw-Zlib/2.202 Low-Level Interface to zlib or zlib-ng compression library ConnectomeWorkbench: ConnectomeWorkbench/1.5.0 Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. Cython: Cython/0.27.3, Cython/0.29.33 Cython is an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). DB: DB/18.1.40 Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. DBD-mysql: DBD-mysql/4.050 Perl binding for MySQL DB_File: DB_File/1.858 Perl5 access to Berkeley DB version 1.x. DBus: DBus/1.14.0 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: DIAMOND/2.1.0 Accelerated BLAST compatible local sequence aligner DMTCP: DMTCP/3.0.0 DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications. DendroPy: DendroPy/4.5.2 A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. Doxygen: Doxygen/1.9.4 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. Drishti: Drishti/3.1 Drishti is an open-source scientific visualisation software designed by Ajay Limaye at the National Computational Infrastructure's VizLab. ELPA: ELPA/2021.11.001, ELPA/2022.05.001 Eigenvalue SoLvers for Petaflop-Applications. EMBOSS: EMBOSS/6.6.0 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. ESMF: ESMF/8.3.0 The Earth System Modeling Framework (ESMF) is a suite of software tools for developing high-performance, multi-component Earth science modeling applications. EasyBuild: EasyBuild/4.7.1, EasyBuild/4.8.0 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: Eigen/3.3.9, Eigen/3.4.0 Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. Emacs: Emacs/28.1 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: FASTX-Toolkit/0.0.14 The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. FDS: FDS/6.7.9 Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. FFTW: FFTW/3.3.10 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. FFTW.MPI: FFTW.MPI/3.3.10 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: FFmpeg/4.4.2, FFmpeg/5.0.1 A complete, cross-platform solution to record, convert and stream audio and video. FLAC: FLAC/1.3.4 FLAC stands for Free Lossless Audio Codec, an audio format similar to MP3, but lossless, meaning that audio is compressed in FLAC without any loss in quality. FLASH: FLASH/2.2.00 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: FLTK/1.3.8 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. FPC: FPC/3.2.2 Free Pascal is a mature, versatile, open source Pascal compiler. FSL: FSL/6.0.6.4 FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. FastANI: FastANI/1.33 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. FastME: FastME/2.1.6.1 FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. FastQC: 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: FastTree/2.1.11 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. Flask: Flask/2.2.2 Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. This module includes the Flask extensions: Flask-Cors FlexiBLAS: FlexiBLAS/3.2.0 FlexiBLAS is a wrapper library that enables the exchange of the BLAS and LAPACK implementation used by a program without recompiling or relinking it. FragGeneScan: FragGeneScan/1.31 FragGeneScan is an application for finding (fragmented) genes in short reads. FreeFEM: FreeFEM/4.12-Python-3.10.4, FreeFEM/4.13-Python-3.10.4 FreeFEM offers a fast interpolation algorithm and a language for the manipulation of data on multiple meshes. FreeImage: FreeImage/3.18.0 FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe. FreeSurfer: FreeSurfer/6.0.1-centos6_x86_64, FreeSurfer/7.3.2-centos8_x86_64 FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. FriBidi: FriBidi/1.0.12 The Free Implementation of the Unicode Bidirectional Algorithm. GATK: GATK/3.7-Java-1.8.0_241, GATK/4.3.0.0-Java-11 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: GCC/11.3.0 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: GCCcore/11.3.0 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,...). GD: GD/2.75 GD.pm - Interface to Gd Graphics Library GDAL: GDAL/3.5.0 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. GDB: GDB/12.1 The GNU Project Debugger GDRCopy: GDRCopy/2.3 A low-latency GPU memory copy library based on NVIDIA GPUDirect RDMA technology. GEOS: GEOS/3.10.3 GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) GL2PS: GL2PS/1.4.2 GL2PS: an OpenGL to PostScript printing library GLM: GLM/0.9.9.8 OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. GLPK: GLPK/5.0 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: GLib/2.72.1 GLib is one of the base libraries of the GTK+ project GLibmm: GLibmm/2.76.0 C++ bindings for Glib GMAP-GSNAP: GMAP-GSNAP/2023-02-17 GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program GMP: GMP/6.2.1 GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. GObject-Introspection: GObject-Introspection/1.72.0 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. GRASP: GRASP/2018 The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms. GROMACS: GROMACS/2023.1, GROMACS/2023.2-CUDA-11.7.0 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 binaries for both single and double precision. It also contains the gmxapi extension for the single precision MPI build. GSL: GSL/2.7 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-bad: GST-plugins-bad/1.20.2 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. GST-plugins-base: GST-plugins-base/1.20.2 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: GStreamer/1.20.2 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. GTDB-Tk: GTDB-Tk/2.3.2 A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. GTK+: GTK+/3.24.23 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. GTK2: GTK2/2.24.33 The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. GTK3: GTK3/3.24.33 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. GTK4: GTK4/4.7.0 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: GTS/0.7.6 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. Gaussian: Gaussian/g16c01-CUDA-11.7.0 Gaussian provides electronic structure modeling. Gdk-Pixbuf: Gdk-Pixbuf/2.42.8 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. GffCompare: GffCompare/0.12.6 GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. Ghostscript: Ghostscript/9.56.1 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. GitPython: GitPython/3.1.27 GitPython is a python library used to interact with Git repositories GlobalArrays: GlobalArrays/5.8.1 Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model GnuCOBOL: GnuCOBOL/3.2 GnuCOBOL (formerly OpenCOBOL) is a free COBOL compiler. cobc translates COBOL source to executable using intermediate C, designated C compiler and linker. Go: Go/1.17.6, Go/1.18.3 Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. Graphene: Graphene/1.10.8 Graphene is a thin layer of types for graphic libraries GraphicsMagick: GraphicsMagick/1.3.36 GraphicsMagick is the swiss army knife of image processing. Graphviz: Graphviz/2.50.0, Graphviz/5.0.0 Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. GtkSourceView: GtkSourceView/3.24.11 GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ widget for multiline text editing. GtkSourceView adds support for syntax highlighting, undo/redo, file loading and saving, search and replace, a completion system, printing, displaying line numbers, and other features typical of a source code editor. Gurobi: Gurobi/10.0.1-Python-3.10.4 The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. HDF: HDF/4.2.15 HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. HDF5: HDF5/1.12.2 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. HEALPix: HEALPix/3.82 Hierarchical Equal Area isoLatitude Pixelation of a sphere. HISAT2: HISAT2/2.2.1 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: HMMER/3.3.2 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. HOOMD-blue: HOOMD-blue/4.0.1-CUDA-11.7.0 HOOMD-blue is a general-purpose particle simulation toolkit, implementing molecular dynamics and hard particle Monte Carlo optimized for fast execution on both GPUs and CPUs. HTSeq: HTSeq/2.0.2 HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments. HTSlib: HTSlib/1.15.1 A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix HarfBuzz: HarfBuzz/4.2.1 HarfBuzz is an OpenType text shaping engine. HyPhy: HyPhy/2.5.33 HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning Hypre: Hypre/2.25.0 Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. ICU: ICU/71.1 ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. IDBA-UD: IDBA-UD/1.1.3 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. IMPUTE2: IMPUTE2/2.3.2_x86_64_dynamic, IMPUTE2/2.3.2_x86_64_static IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 IPython: IPython/8.5.0 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. IQ-TREE: IQ-TREE/2.2.2.6 Efficient phylogenomic software by maximum likelihood IRFinder-S: IRFinder-S/2.0.1 IRFinder detects intron retention from RNA-Seq experiments. ISA-L: ISA-L/2.30.0 Intelligent Storage Acceleration Library ISL: ISL/0.24 isl is a library for manipulating sets and relations of integer points bounded by linear constraints. ITK: ITK/5.2.1 Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. ImageMagick: ImageMagick/7.1.0-37 ImageMagick is a software suite to create, edit, compose, or convert bitmap images Imath: Imath/3.1.5 Imath is a C++ and python library of 2D and 3D vector, matrix, and math operations for computer graphics Infernal: Infernal/1.1.4 Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. IntelPython: IntelPython/3.9.16-2023.1.0 Intel® Distribution for Python. Powered by Anaconda. Accelerating Python* performance on modern architectures from Intel. InterProScan: InterProScan/5.55-88.0 InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource [code only: libraries and external binaries but no data]. JAGS: JAGS/4.3.1 JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation JasPer: JasPer/2.0.33 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: Java/1.8.0_241, Java/8.372, Java/11.0.18, Java/17.0.6 Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. Jellyfish: Jellyfish/2.3.0 Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. JsonCpp: JsonCpp/1.9.5 JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. Judy: Judy/1.0.5 A C library that implements a dynamic array. Julia: Julia/1.8.5-linux-x86_64, Julia/1.9.3-linux-x86_64 Julia is a high-level, high-performance dynamic programming language for numerical computing JupyterLab: JupyterLab/3.5.0 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. KMC: KMC/3.2.1 KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. KaHIP: KaHIP/3.14 The graph partitioning framework KaHIP -- Karlsruhe High Quality Partitioning. Kraken2: Kraken2/2.1.2 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. LAME: LAME/3.100 LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. LAMMPS: LAMMPS/23Jun2022-kokkos-CUDA-11.7.0, LAMMPS/23Jun2022-kokkos LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality. LANDIS-II: LANDIS-II/7.0 The LANDIS-II forest landscape model simulates future forests (both trees and shrubs) at decadal to multi-century time scales and spatial scales spanning hundreds to millions of hectares. LAPACK: LAPACK/3.10.1 LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations, least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems. LASTZ: LASTZ/1.04.03 LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. LIBSVM: LIBSVM/3.30 LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. LLVM: LLVM/14.0.3 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: LMDB/0.9.29 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. LSD2: LSD2/2.3 Least-squares methods to estimate rates and dates from phylogenies LZO: LZO/2.10 Portable lossless data compression library LibLZF: LibLZF/3.6 LibLZF is a very small data compression library. It consists of only two .c and two .h files and is very easy to incorporate into your own programs. The compression algorithm is very, very fast, yet still written in portable C. LibTIFF: LibTIFF/4.3.0 tiff: Library and tools for reading and writing TIFF data files Lighter: Lighter/1.1.2 Fast and memory-efficient sequencing error corrector LittleCMS: LittleCMS/2.13.1 Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. Lua: Lua/5.4.4 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: M4/1.4.19 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: MACS2/2.2.8 Model Based Analysis for ChIP-Seq data MAFFT: MAFFT/7.505-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 <∼30,000 sequences), etc. MATLAB: MATLAB/2023a_Update_1, MATLAB/2023a MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. MCL: MCL/14.137 The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. MCR: MCR/R2016a The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. MEGAHIT: MEGAHIT/1.2.9 An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph MEME: MEME/5.5.3 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. META: META/1.7 META is a program for the meta analysis of genome-wide association studies. The program is designed to synthesizing the evidence from different association studies. Particularly, the program is able to work seamlessly with the output of SNPTEST. METIS: METIS/5.1.0 METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. MINC: MINC/2.4.03 Medical Image NetCDF or MINC isn't netCDF. MMseqs2: MMseqs2/14-7e284 MMseqs2: ultra fast and sensitive search and clustering suite MPC: MPC/1.2.1 Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal. MPFR: MPFR/4.1.0 The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. MPICH: MPICH/4.1.2 MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (MPI-1, MPI-2 and MPI-3). MRtrix: MRtrix/3.0.4 MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. MRtrix3Tissue: MRtrix3Tissue/5.2.9-Python-2.7.18 MRtrix3Tissue is a fork of the MRtrix3 project. It aims to add capabilities for 3-Tissue CSD modelling and analysis to a complete version of the MRtrix3 software. MUMPS: MUMPS/5.5.1-metis A parallel sparse direct solver MUSCLE: MUSCLE/5.1.0 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. MaSuRCA: MaSuRCA/4.1.0 MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). Mako: Mako/1.2.0 A super-fast templating language that borrows the best ideas from the existing templating languages Mambaforge: Mambaforge/23.1.0-4 Mambaforge is based on miniforge and allows you to install the conda package manager with the following features pre-configured: conda-forge set as the default (and only) channel, and support for Mamba in place of Conda. MariaDB: MariaDB/10.9.3 MariaDB is an enhanced, drop-in replacement for MySQL. Included engines: myISAM, Aria, InnoDB, RocksDB, TokuDB, OQGraph, Mroonga. Mash: Mash/2.3 Fast genome and metagenome distance estimation using MinHash Mathematica: Mathematica/13.2.1 Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. Maven: Maven/3.9.3 Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. MaxBin: MaxBin/2.2.7 MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. Maxima: Maxima/5.47.0 Maxima is a system for the manipulation of symbolic and numerical expressions. Mercurial: Mercurial/6.2 Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. Meryl: Meryl/1.4 Meryl is a tool for creating and working with DNA sequence k-mers. Mesa: Mesa/22.0.3 Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. Meson: Meson/0.62.1, Meson/0.64.0 Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. MetaEuk: MetaEuk/6 MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Miniconda2: Miniconda2/4.7.10 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. Miniconda3: Miniconda3/22.11.1-1 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: Mono/6.12.0.122 An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. MosiacHunter: MosiacHunter/1.0.0 A tool to detect postzygotic single-nucleotide mosaicism from unpaired, trio, or paired samples. MrBayes: MrBayes/3.2.7a MrBayes is a program for the Bayesian estimation of phylogeny. MultiQC: MultiQC/1.14 Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles an HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. Multiwell: Multiwell/2021, Multiwell/2023.1-u Calculates time dependent concentrations, reaction yields, vibrational distributions, and rate constants as functions of temperature and pressure for multi-well, multi-channel unimolecular reactions systems. NAMD: NAMD/2.14-CUDA-11.7.0 NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NASM: NASM/2.15.05 NASM: General-purpose x86 assembler NCCL: NCCL/2.12.12-CUDA-11.7.0, NCCL/2.18.3-CUDA-12.2.0 The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. NCO: NCO/5.1.3 The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. NGS: NGS/2.11.2 NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. NIfTI: NIfTI/2.0.0 Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. NLTK: NLTK/3.7 NLTK is a leading platform for building Python programs to work with human language data. NLopt: NLopt/2.7.1 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: NSPR/4.34 Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. NSS: NSS/3.79 Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. NVHPC: NVHPC/22.11-CUDA-11.7.0 C, C++ and Fortran compilers included with the NVIDIA HPC SDK (previously: PGI) Nektar++: Nektar++/5.3.0 Nektar++ is a tensor product based finite element package designed to allow one to construct efficient classical low polynomial order h-type solvers (where h is the size of the finite element) as well as higher p-order piecewise polynomial order solvers. Nextflow: Nextflow/23.04.2 Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data Nim: Nim/1.6.6 Nim is a systems and applications programming language. Ninja: Ninja/1.10.2 Ninja is a small build system with a focus on speed. ORCA: ORCA/5.0.4 ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Octave: Octave/7.1.0 GNU Octave is a high-level interpreted language, primarily intended for numerical computations. OpenBLAS: OpenBLAS/0.3.20 OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. OpenCV: OpenCV/4.6.0-contrib OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. Includes extra modules for OpenCV from the contrib repository. OpenEXR: OpenEXR/3.1.5 OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications OpenFOAM: OpenFOAM/v2206, OpenFOAM/6 OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. OpenJPEG: OpenJPEG/2.5.0 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: OpenMPI/4.1.4 The Open MPI Project is an open source MPI-3 implementation. OpenMolcas: OpenMolcas/22.10 OpenMolcas is a quantum chemistry software package. OpenPGM: OpenPGM/5.2.122 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. OpenSSL: OpenSSL/1.1 The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. OpenSlide: OpenSlide/3.4.1-largefiles OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). OpenVDB: OpenVDB/10.0.1 OpenVDB is an Academy Award-winning open-source C++ library comprising a novel hierarchical data structure and a suite of tools for the efficient storage and manipulation of sparse volumetric data discretized on three-dimensional grids. It was developed by DreamWorks Animation for use in volumetric applications typically encountered in feature film production and is now maintained by the Academy Software Foundation (ASWF). OptiX: OptiX/7.6.0 OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms. OrthoFinder: OrthoFinder/2.5.5 OrthoFinder: phylogenetic orthology inference for comparative genomics PAML: PAML/4.10.5 PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PCRE: PCRE/8.45 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PCRE2: PCRE2/10.40 The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. PETSc: PETSc/3.17.4, PETSc/3.18.3, PETSc/3.19.2 PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. PICI-LIGGGHTS: PICI-LIGGGHTS/3.8.1 UoB Positron Imaging Centre's Improved LIGGGHTS distribution with an emphasis on the Python interface. PLINK: PLINK/1.9b_6.21-x86_64, PLINK/2.00a3.6 Whole-genome association analysis toolset PLUMED: PLUMED/2.8.1 PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. PMIx: PMIx/3.2.3, PMIx/4.2.2 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 - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. POV-Ray: POV-Ray/3.7.0.10 The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. PROJ: PROJ/9.0.0 Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates Pandoc: Pandoc/3.1.2 If you need to convert files from one markup format into another, pandoc is your swiss-army knife Pango: Pango/1.50.7 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. ParMETIS: ParMETIS/4.0.3 ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. ParaView: ParaView/5.10.1-mpi ParaView is a scientific parallel visualizer. Perl: Perl/5.34.1-minimal, Perl/5.34.1 Larry Wall's Practical Extraction and Report Language This is a minimal build without any modules. Should only be used for build dependencies. Pillow: Pillow/9.1.1 Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. Pillow-SIMD: Pillow-SIMD/9.2.0 Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. Pilon: Pilon/1.23-Java-11 Pilon is an automated genome assembly improvement and variant detection tool PnetCDF: PnetCDF/1.12.3 Parallel netCDF: A Parallel I/O Library for NetCDF File Access PolSpice: PolSpice/3.7.5 PolSpice (aka Spice) is a tool to statistically analyze Cosmic Microwave Background (CMB) data, as well as any other diffuse data pixelized on the sphere. PostgreSQL: PostgreSQL/14.4 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. PyBioLib: PyBioLib/1.1.988 PyBioLib is a Python package for running BioLib applications from Python scripts and the command line. BioLib is a library of biological data science applications. Applications on BioLib range from small bioinformatics utilities to state-of-the-art machine learning algorithms for predicting characteristics of biological molecules. PyCairo: PyCairo/1.21.0 Python bindings for the cairo library PyGObject: PyGObject/3.42.1 PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more. PyMOL: PyMOL/2.5.0 PyMOL is a Python-enhanced molecular graphics tool. It excels at 3D visualization of proteins, small molecules, density, surfaces, and trajectories. It also includes molecular editing, ray tracing, and movies. Open Source PyMOL is free to everyone! PyQt5: PyQt5/5.15.5 PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. This bundle includes PyQtWebEngine, a set of Python bindings for The Qt Company’s Qt WebEngine framework. PyTorch: PyTorch/1.12.0, PyTorch/1.12.1-CUDA-11.7.0, PyTorch/1.12.1 Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. PyYAML: PyYAML/6.0 PyYAML is a YAML parser and emitter for the Python programming language. Pysam: Pysam/0.19.1 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: Python/2.7.18-bare, Python/2.7.18, Python/3.10.4-bare, Python/3.10.4 Python is a programming language that lets you work more quickly and integrate your systems more effectively. QIIME2: QIIME2/2022.11 QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. QUAST: QUAST/5.2.0 QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. Qhull: Qhull/2020.2 Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. Qt5: Qt5/5.15.2, Qt5/5.15.5 Qt is a comprehensive cross-platform C++ application framework. QuantumESPRESSO: QuantumESPRESSO/7.1 Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). Qwt: Qwt/6.2.0 The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. R: R/4.2.1-bare, R/4.2.1, R/4.2.2 R is a free software environment for statistical computing and graphics. R-bundle-Bioconductor: R-bundle-Bioconductor/3.16-R-4.2.2 Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. RASPA2: RASPA2/2.0.47 RASPA is a software package for simulating adsorption and diffusion of molecules in flexible nanoporous materials. RAxML: RAxML/8.2.12-hybrid-avx2 RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. RE2: RE2/2022-06-01 RE2 is a fast, safe, thread-friendly alternative to backtracking regular expression engines like those used in PCRE, Perl, and Python. It is a C++ library. RIblast: RIblast/1.2.0 RIblast is ultrafast RNA-RNA interaction prediction software based on seed-and-extension algorithm for comprehensive lncRNA interactome analysis. ROOT: ROOT/6.26.10 The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. RSEM: RSEM/1.3.3 RNA-Seq by Expectation-Maximization RStudio-Server: RStudio-Server/2022.07.2+576-Java-11-R-4.2.1 This is the RStudio Server version. RStudio is a set of integrated tools designed to help you be more productive with R. The server can be started with: rserver --server-daemonize=0 --www-port=8787 If you need a database config one can be created with: MYTMP=`mktemp -d` && echo -e "provider=sqlite\ndirectory=${MYTMP}/sqlite" > "${MYTMP}/db.conf" and then used with: rserver ... --database-config-file="${MYTMP}/db.conf" RapidJSON: RapidJSON/1.1.0 A fast JSON parser/generator for C++ with both SAX/DOM style API Rust: Rust/1.60.0, Rust/1.65.0 Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. SAMtools: SAMtools/1.13, SAMtools/1.16.1 SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. SCOTCH: SCOTCH/7.0.1 Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. SCons: SCons/4.4.0 SCons is a software construction tool. SDL2: SDL2/2.0.22 SDL: Simple DirectMedia Layer, a cross-platform multimedia library SEPP: SEPP/4.5.1 SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees. SHAPEIT: SHAPEIT/2.r904.glibcv2.17 SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. SKESA: SKESA/2.4.0_saute.1.3.0_1 SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs. SLEPc: SLEPc/3.17.2, SLEPc/3.18.3 SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. SLiM: SLiM/4.0.1 SLiM is an evolutionary simulation framework that combines a powerful engine for population genetic simulations with the capability of modeling arbitrarily complex evolutionary scenarios. SOCI: SOCI/4.0.3 SOCI is a database access library for C++ that makes the illusion of embedding SQL queries in the regular C++ code, staying entirely within the Standard C++. SPAdes: SPAdes/3.15.5 Genome assembler for single-cell and isolates data sets SQLite: SQLite/3.38.3, SQLite/3.42.0 SQLite: SQL Database Engine in a C Library SRA-Toolkit: SRA-Toolkit/3.0.3, SRA-Toolkit/3.0.5 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 SSW: SSW/1.1 SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages. We also provide a software that can do protein and genome alignment directly. Current version of our implementation is ~50 times faster than an ordinary Smith-Waterman. It can return the Smith-Waterman score, alignment location and traceback path (cigar) of the optimal alignment accurately; and return the sub-optimal alignment score and location heuristically. STAR: STAR/2.7.10b STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. SUNDIALS: SUNDIALS/6.3.0 SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers SUPPA: SUPPA/2.3 A tool to study splicing across multiple conditions at high speed and accuracy. SWIG: SWIG/4.0.2 SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. Salmon: Salmon/1.9.0 Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. ScaFaCoS: ScaFaCoS/1.0.1 ScaFaCoS is a library of scalable fast coulomb solvers. ScaLAPACK: ScaLAPACK/2.2.0-fb The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. SciPy-bundle: SciPy-bundle/2022.05test, SciPy-bundle/2022.05 Bundle of Python packages for scientific software Seaborn: Seaborn/0.12.1 Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. SeqKit: SeqKit/2.3.1 SeqKit - a cross-platform and ultrafast toolkit for FASTA/Q file manipulation SeqLib: SeqLib/1.2.0 C++ interface to HTSlib, BWA-MEM and Fermi. Serf: Serf/1.3.9 The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library Stata: Stata/16-legacy Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. Subread: Subread/2.0.4 High performance read alignment, quantification and mutation discovery Subversion: Subversion/1.14.1, Subversion/1.14.2 Subversion is an open source version control system. SuiteSparse: SuiteSparse/5.13.0-METIS-5.1.0 SuiteSparse is a collection of libraries manipulate sparse matrices. SuperLU_DIST: SuperLU_DIST/8.1.0 SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. Szip: Szip/2.1.1 Szip compression software, providing lossless compression of scientific data TCLAP: TCLAP/1.2.5 TCLAP is a small, flexible library that provides a simple interface for defining and accessing command line arguments. It was intially inspired by the user friendly CLAP libary. TRF: TRF/4.09.1 Tandem Repeats Finder: a program to analyze DNA sequences. TRUST4: TRUST4/1.0.7 Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. TRUST4 performs de novo assembly on V, J, C genes including the hypervariable complementarity-determining region 3 (CDR3) and reports consensus of BCR/TCR sequences. TRUST4 then realigns the contigs to IMGT reference gene sequences to report the corresponding information. TRUST4 supports both single-end and paired-end sequencing data with any read length. Tcl: Tcl/8.6.12, Tcl/8.6.13 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: TensorFlow/2.11.0-CUDA-11.7.0, TensorFlow/2.11.0 An open-source software library for Machine Intelligence Tk: Tk/8.6.12 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: Tkinter/3.10.4 Tkinter module, built with the Python buildsystem TopHat: TopHat/2.1.2 TopHat is a fast splice junction mapper for RNA-Seq reads. TractSeg: TractSeg/2.8 Tool for fast and accurate white matter bundle segmentation from Diffusion MRI. It can create bundle segmentations, segmentations of the endregions of bundles and Tract Orientation Maps (TOMs). Moreover, it can do tracking on the TOMs creating bundle-specific tractogram and do Tractometry analysis on those. TransDecoder: TransDecoder/5.5.0 TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. Trim_Galore: Trim_Galore/0.6.10 Trim Galore! is a wrapper script to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files (for directional, non-directional (or paired-end) sequencing). Trimmomatic: 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: Trinity/2.15.1 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. Trinotate: Trinotate/4.0.1 Trinotate is a comprehensive annotation suite designed for automatic functional annotation of transcriptomes, particularly de novo assembled transcriptomes, from model or non-model organisms. Trinotate makes use of a number of different well referenced methods for functional annotation including homology search to known sequence data (BLAST+/SwissProt), protein domain identification (HMMER/PFAM), protein signal peptide and transmembrane domain prediction (signalP/tmHMM), and leveraging various annotation databases (eggNOG/GO/Kegg databases). All functional annotation data derived from the analysis of transcripts is integrated into a SQLite database which allows fast efficient searching for terms with specific qualities related to a desired scientific hypothesis or a means to create a whole annotation report for a transcriptome. UCC: UCC/1.0.0 UCC (Unified Collective Communication) is a collective communication operations API and library that is flexible, complete, and feature-rich for current and emerging programming models and runtimes. UCX: UCX/1.13.1 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications UCX-CUDA: UCX-CUDA/1.13.1-CUDA-11.7.0, UCX-CUDA/1.13.1-CUDA-12.2.0 Unified Communication X An open-source production grade communication framework for data centric and high-performance applications This module adds the UCX CUDA support. UDUNITS: UDUNITS/2.2.28 UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. US-Align: US-Align/20221221 US-align: universal structure alignment of monomeric and complex proteins and nucleic acids UnZip: UnZip/6.0 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: VCFtools/0.1.16 The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. VEP: VEP/107 Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP. VMD: VMD/1.9.4a57 VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VTK: VTK/9.2.2 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. VTune: VTune/2022.3.0 Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. Valgrind: Valgrind/3.20.0 Valgrind: Debugging and profiling tools VarScan: VarScan/2.4.4-Java-11 Variant calling and somatic mutation/CNV detection for next-generation sequencing data Velvet: Velvet/1.2.10-mt-kmer_191 Sequence assembler for very short reads Voro++: Voro++/0.4.6 Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. Wayland: Wayland/1.20.0 Wayland is a project to define a protocol for a compositor to talk to its clients as well as a library implementation of the protocol. The compositor can be a standalone display server running on Linux kernel modesetting and evdev input devices, an X application, or a wayland client itself. The clients can be traditional applications, X servers (rootless or fullscreen) or other display servers. X11: X11/20220504 The X Window System (X11) is a windowing system for bitmap displays XML-Compile: XML-Compile/1.63 Perl module for compilation based XML processing XML-LibXML: XML-LibXML/2.0207 Perl binding for libxml2 XZ: XZ/5.2.5-test, XZ/5.2.5, XZ/5.4.2 xz: XZ utilities XlsxWriter: XlsxWriter/3.0.8 A Python module for creating Excel XLSX files Xvfb: Xvfb/1.20.13, Xvfb/21.1.3 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: Yasm/1.3.0 Yasm: Complete rewrite of the NASM assembler with BSD license Z3: Z3/4.10.2 Z3 is a theorem prover from Microsoft Research. ZeroMQ: ZeroMQ/4.3.4 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: Zip/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 ant: ant/1.10.11-Java-11, ant/1.10.12-Java-11 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. any2fasta: any2fasta/0.4.2 Convert various sequence formats to FASTA archspec: archspec/0.1.4 A library for detecting, labeling, and reasoning about microarchitectures argtable: argtable/2.13 Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. arpack-ng: arpack-ng/3.8.0 ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. arrow-R: arrow-R/8.0.0-R-4.2.2 R interface to the Apache Arrow C++ library assimp: assimp/5.2.5 Open Asset Import Library (assimp) is a library to import and export various 3d-model-formats including scene-post-processing to generate missing render data. at-spi2-atk: at-spi2-atk/2.38.0 AT-SPI 2 toolkit bridge at-spi2-core: at-spi2-core/2.48.3 Assistive Technology Service Provider Interface. awscli: awscli/2.11.21 Universal Command Line Environment for AWS barrnap: barrnap/0.9 Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes. bcl2fastq2: bcl2fastq2/2.20.0 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: beagle-lib/3.1.2-CUDA-11.7.0, beagle-lib/4.0.0-CUDA-11.7.0, beagle-lib/4.0.0 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: binutils/2.38 binutils: GNU binary utilities bioawk: bioawk/1.0 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. bokeh: bokeh/2.4.3 Statistical and novel interactive HTML plots for Python bwa-mem2: bwa-mem2/2.2.1 Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. bzip2: bzip2/1.0.8 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. cURL: cURL/7.83.0 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: cairo/1.17.4 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 code-server: code-server/4.9.1 Run VS Code on any machine anywhere and access it in the browser. coverm: coverm/0.6.1-linux-x86_64 CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. cppy: cppy/1.2.1 A small C++ header library which makes it easier to write Python extension modules. The primary feature is a PyObject smart pointer which automatically handles reference counting and provides convenience methods for performing common object operations. cuDNN: cuDNN/8.4.1.50-CUDA-11.7.0, cuDNN/8.9.3.28-CUDA-12.2.0 The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. cutadapt: cutadapt/4.2 Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. dashing: dashing/1.0 Dashing sketches and computes distances between fasta and fastq data. dask: dask/2022.10.0 Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. datamash: datamash/1.8 GNU datamash performs basic numeric, textual and statistical operations on input data files dcm2niix: dcm2niix/1.0.20220720 dcm2niix is designed to convert neuroimaging data from the DICOM format to the NIfTI format. deepTools: deepTools/3.5.2 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. dill: dill/0.3.6 dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy. dorado: dorado/0.3.1-CUDA-11.7.0 Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. dotNET-SDK: dotNET-SDK/6.0.101-linux-x64 .NET is a free, cross-platform, open source developer platform for building many different types of applications. double-conversion: double-conversion/3.2.0 Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. eagle: eagle/1.1.3 Explicit Alternative Genome Likelihood Evaluator ecCodes: ecCodes/2.27.0 ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). eggnog-mapper: eggnog-mapper/2.1.9 EggNOG-mapper is a tool for fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database (http://eggnog5.embl.de) to transfer functional information from fine-grained orthologs only. Common uses of eggNOG-mapper include the annotation of novel genomes, transcriptomes or even metagenomic gene catalogs. elfutils: elfutils/0.187 The elfutils project provides libraries and tools for ELF files and DWARF data. expat: expat/2.4.8 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) expecttest: expecttest/0.1.3 This library implements expect tests (also known as "golden" tests). Expect tests are a method of writing tests where instead of hard-coding the expected output of a test, you run the test to get the output, and the test framework automatically populates the expected output. If the output of the test changes, you can rerun the test with the environment variable EXPECTTEST_ACCEPT=1 to automatically update the expected output. fast5: fast5/0.6.5 A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data. fastGEAR: fastGEAR/20161216 Inference of recent and ancestral recombination between divergent lineages in bacteria. fastahack: fastahack/1.0.0 Utilities for indexing and sequence extraction from FASTA files. fastp: fastp/0.23.2 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-pair: fastq-pair/1.0 Match up paired end fastq files quickly and efficiently. fermi-lite: fermi-lite/20190320 Standalone C library for assembling Illumina short reads in small regions. ffnvcodec: ffnvcodec/11.1.5.2 FFmpeg nvidia headers. Adds support for nvenc and nvdec. Requires Nvidia GPU and drivers to be present (picked up dynamically). file: file/5.43 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. filevercmp: filevercmp/20191210 filevercmp function as in sort --version-sort. flatbuffers: flatbuffers/2.0.7 FlatBuffers: Memory Efficient Serialization Library Includes the Flatbuffers compiler, C/C++ bindings and Python runtime library. flex: flex/2.6.4 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: fontconfig/2.14.0 Fontconfig is a library designed to provide system-wide font configuration, customization and application access. foss: foss/2022a GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. freebayes: freebayes/1.3.6 Bayesian haplotype-based genetic polymorphism discovery and genotyping. freeglut: freeglut/3.2.2 freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. freetype: freetype/2.12.1 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. fsom: fsom/20141119 A tiny C library for managing SOM (Self-Organizing Maps) neural networks. g2clib: g2clib/1.7.0 Library contains GRIB2 encoder/decoder ('C' version). g2lib: g2lib/3.2.0 Library contains GRIB2 encoder/decoder and search/indexing routines. gawk: gawk/5.1.1 The awk utility interprets a special-purpose programming language that makes it possible to handle simple data-reformatting jobs with just a few lines of code. gettext: gettext/0.21, gettext/0.21.1 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 gfbf: gfbf/2022a GNU Compiler Collection (GCC) based compiler toolchain, including FlexiBLAS (BLAS and LAPACK support) and (serial) FFTW. gffread: gffread/0.12.7 GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. giflib: giflib/5.2.1 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: git/2.36.0-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. glew: glew/2.1.0 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. gmsh: gmsh/4.11.1 Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. gnuplot: gnuplot/5.4.4 Portable interactive, function plotting utility gompi: gompi/2022a GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. googletest: googletest/1.11.0 Google's framework for writing C++ tests on a variety of platforms gperf: gperf/3.1 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: graphite2/1.3.14 Graphite is a "smart font" system developed specifically to handle the complexities of lesser-known languages of the world. groff: groff/1.22.4 Groff (GNU troff) is a typesetting system that reads plain text mixed with formatting commands and produces formatted output. gubbins: gubbins/2.4.0 Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences. gzip: gzip/1.12 gzip (GNU zip) is a popular data compression program as a replacement for compress h5py: h5py/3.7.0 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: help2man/1.49.2 help2man produces simple manual pages from the '--help' and '--version' output of other commands. hifiasm: hifiasm/0.19.5 Hifiasm: a haplotype-resolved assembler for accurate Hifi reads. hwloc: hwloc/2.7.1, hwloc/2.8.0 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: hypothesis/6.46.7 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. imkl: imkl/2022.1.0 Intel oneAPI Math Kernel Library intel-compilers: intel-compilers/2022.1.0 Intel C, C++ & Fortran compilers (classic and oneAPI) intervaltree: intervaltree/0.1 An interval tree can be used to efficiently find a set of numeric intervals overlapping or containing another interval. This library provides a basic implementation of an interval tree using C++ templates, allowing the insertion of arbitrary types into the tree. intltool: intltool/0.51.0 intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. iomkl: iomkl/2022a Compiler toolchain including Intel compilers, Open MPI and Intel Math Kernel Library (MKL). iompi: iompi/2022a Intel C/C++ and Fortran compilers, alongside Open MPI. jbigkit: jbigkit/2.1 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: jemalloc/5.2.1, jemalloc/5.3.0 jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. joe: joe/4.6 JOE is a full featured terminal-based screen editor. jq: jq/1.5 jq is a lightweight and flexible command-line JSON processor. jupyter-contrib-nbextensions: jupyter-contrib-nbextensions/0.7.0 A collection of various notebook extensions for Jupyter jupyter-server: jupyter-server/1.21.0 The Jupyter Server provides the backend (i.e. the core services, APIs, and REST endpoints) for Jupyter web applications like Jupyter notebook, JupyterLab, and Voila. kallisto: kallisto/0.48.0 kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. kim-api: kim-api/2.3.0 Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. kineto: kineto/0.4.0 A CPU+GPU Profiling library that provides access to timeline traces and hardware performance counters libGLU: libGLU/9.0.2 The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. libQGLViewer: libQGLViewer/2.6.4 libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers. libRmath: libRmath/4.2.1 The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications. libaec: libaec/1.0.6 Libaec provides fast lossless compression of 1 up to 32 bit wide signed or unsigned integers (samples). The library achieves best results for low entropy data as often encountered in space imaging instrument data or numerical model output from weather or climate simulations. While floating point representations are not directly supported, they can also be efficiently coded by grouping exponents and mantissa. libaio: libaio/0.3.112 Asynchronous input/output library that uses the kernels native interface. libarchive: libarchive/3.6.1 Multi-format archive and compression library libcerf: libcerf/2.1 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. libdap: libdap/3.20.11 A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. libdeflate: libdeflate/1.10 Heavily optimized library for DEFLATE/zlib/gzip compression and decompression. libdrm: libdrm/2.4.110 Direct Rendering Manager runtime library. libepoxy: libepoxy/1.5.10 Epoxy is a library for handling OpenGL function pointer management for you libevent: libevent/2.1.12 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. libexif: libexif/0.6.24 A library for parsing, editing, and saving EXIF data. libfabric: libfabric/1.15.1 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. libffcall: libffcall/2.4 GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters libffi: libffi/3.4.2, libffi/3.4.4 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. libgd: libgd/2.3.3 GD is an open source code library for the dynamic creation of images by programmers. libgdiplus: libgdiplus/6.1 Libgdiplus is the Mono library that provides a GDI+-compatible API on non-Windows operating systems. libgeotiff: libgeotiff/1.7.1 Library for reading and writing coordinate system information from/to GeoTIFF files libgit2: libgit2/1.4.3 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: libglvnd/1.4.0 libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. libgtextutils: libgtextutils/0.7 ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream libharu: libharu/2.3.0 libHaru is a free, cross platform, open source library for generating PDF files. libiconv: libiconv/1.17 Libiconv converts from one character encoding to another through Unicode conversion libidn2: libidn2/2.3.2 Libidn2 implements the revised algorithm for internationalized domain names called IDNA2008/TR46. libjpeg-turbo: libjpeg-turbo/2.1.3 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. libogg: libogg/1.3.5 Ogg is a multimedia container format, and the native file and stream format for the Xiph.org multimedia codecs. libopus: libopus/1.3.1 Opus is a totally open, royalty-free, highly versatile audio codec. Opus is unmatched for interactive speech and music transmission over the Internet, but is also intended for storage and streaming applications. It is standardized by the Internet Engineering Task Force (IETF) as RFC 6716 which incorporated technology from Skype’s SILK codec and Xiph.Org’s CELT codec. libpciaccess: libpciaccess/0.16 Generic PCI access library. libpng: libpng/1.6.37 libpng is the official PNG reference library libreadline: libreadline/8.1.2, libreadline/8.2 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. libsigc++: libsigc++/3.4.0 The libsigc++ package implements a typesafe callback system for standard C++. libsigsegv: libsigsegv/2.14 GNU libsigsegv is a library for handling page faults in user mode. libsndfile: libsndfile/1.1.0 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: libsodium/1.0.18 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. libtirpc: libtirpc/1.3.2 Libtirpc is a port of Suns Transport-Independent RPC library to Linux. libtool: libtool/2.4.7 GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. libunwind: libunwind/1.6.2 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 libvorbis: libvorbis/1.3.7 Ogg Vorbis is a fully open, non-proprietary, patent-and-royalty-free, general-purpose compressed audio format libwebp: libwebp/1.2.4 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. libxc: libxc/5.2.3 Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. libxml++: libxml++/5.0.3 libxml++ is a C++ wrapper for the libxml XML parser library. libxml2: libxml2/2.9.10, libxml2/2.9.13, libxml2/2.10.3 Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). libxslt: libxslt/1.1.34 Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). libyaml: libyaml/0.2.5 LibYAML is a YAML parser and emitter written in C. lmod: lmod Lmod: An Environment Module System lpsolve: lpsolve/5.5.2.11 Mixed Integer Linear Programming (MILP) solver lxml: lxml/4.9.1 The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. lz4: lz4/1.9.3 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. magma: magma/2.6.2-CUDA-11.7.0 The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. make: make/4.3 GNU version of make utility makedepend: makedepend/1.0.7 The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. makeinfo: makeinfo/6.7, makeinfo/6.8 makeinfo is part of the Texinfo project, the official documentation format of the GNU project. manta: manta/1.6.0 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: matplotlib/3.5.2 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. mediaflux-data-mover: mediaflux-data-mover/current mediaflux-data-mover is a data transfer tool for uploading and/or downloading data from a Mediaflux server using a shareable token. mediaflux-explorer: mediaflux-explorer/current mediaflux-explorer is a Java-based GUI application focusing uploads, downloads, queries and sharing of data. minc-stuffs: minc-stuffs/0.1.25 minc-stuffs is repository that houses scripts and bits of code that are useful for performing calculations on and o therwise extracting information from minc files. minc-toolkit: minc-toolkit/1.9.18.2 Medical Image NetCDF or MINC isn't netCDF. minigraph: minigraph/0.20 Minigraph is a sequence-to-graph mapper and graph constructor. minimap2: minimap2/2.24 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. mm-common: mm-common/1.0.5 The mm-common module provides the build infrastructure and utilities shared among the GNOME C++ binding libraries. motif: motif/2.3.8 Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. mpi4py: mpi4py/3.1.4 MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. multichoose: multichoose/1.0.3 generate multiset combinations (n multichoose k). nanopolish: nanopolish/0.13.3 Software package for signal-level analysis of Oxford Nanopore sequencing data. ncbi-vdb: ncbi-vdb/2.11.2, ncbi-vdb/3.0.2, ncbi-vdb/3.0.5 The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. ncdf4: ncdf4/1.17-R-4.2.2 ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files ncurses: ncurses/6.2, ncurses/6.3, ncurses/6.4 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. ncview: ncview/2.1.8 Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. netCDF: netCDF/4.9.0 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. netCDF-C++4: netCDF-C++4/4.3.1 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. netCDF-Fortran: netCDF-Fortran/4.6.0 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: nettle/3.8 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: networkx/2.8.4 NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. nlohmann_json: nlohmann_json/3.10.5 JSON for Modern C++ nodejs: nodejs/16.15.1 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. nsync: nsync/1.25.0 nsync is a C library that exports various synchronization primitives, such as mutexes numactl: numactl/2.0.14, numactl/2.0.16 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: numba/0.56.4 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: numexpr/2.8.4 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. occt: occt/7.5.0p1 Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications. p7zip: p7zip/17.04 p7zip is a quick port of 7z.exe and 7za.exe (CLI version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio. parallel: parallel/20220722 parallel: Build and execute shell commands in parallel parsnp: parsnp/1.5.3 Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. picard: picard/2.25.1-Java-11, picard/3.0.0-Java-17 A set of tools (in Java) for working with next generation sequencing data in the BAM format. pigz: pigz/2.7 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. pixman: pixman/0.40.0 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: pkg-config/0.29.2 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). pkgconf: pkgconf/1.8.0, pkgconf/1.9.5 pkgconf is a program which helps to configure compiler and linker flags for development libraries. It is similar to pkg-config from freedesktop.org. pkgconfig: pkgconfig/1.5.5-python pkgconfig is a Python module to interface with the pkg-config command line tool plotly.py: plotly.py/5.12.0 An open-source, interactive graphing library for Python pocl: pocl/1.8 Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard poppler: poppler/22.12.0 Poppler is a PDF rendering library pplacer: pplacer/1.1.alpha19 Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. prodigal: prodigal/2.6.3 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: prokka/1.14.5 Prokka is a software tool for the rapid annotation of prokaryotic genomes. protobuf: protobuf/3.19.4 Google Protocol Buffers protobuf-python: protobuf-python/3.19.4 Python Protocol Buffers runtime library. pyBigWig: pyBigWig/0.3.18 A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. pybind11: pybind11/2.9.2 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. pydantic: pydantic/1.10.4 Data validation and settings management using Python type hinting. pyminc: pyminc/0.57 A python interface to the MINC 2 library, allowing use of numpy arrays to access MINC data. python-isal: python-isal/1.1.0 Faster zlib and gzip compatible compression and decompression by providing python bindings for the isa-l library. qrupdate: qrupdate/1.1.2 qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. re2c: re2c/2.2 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. rgdal: rgdal/1.6-6 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. ruamel.yaml: ruamel.yaml/0.17.21 ruamel.yaml is a YAML 1.2 loader/dumper package for Python. samclip: samclip/0.4.0 Filter SAM file for soft and hard clipped alignments. scikit-bio: scikit-bio/0.5.7 scikit-bio is an open-source, BSD-licensed Python 3 package providing data structures, algorithms and educational resources for bioinformatics. scikit-build: scikit-build/0.15.0 Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions. scikit-learn: scikit-learn/1.1.2 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. screen_assembly: screen_assembly/1.2.7 Pipeline that screens for presence of genes of interest (GOI) in bacterial assemblies. seqtk: seqtk/1.3 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. settarg: settarg The settarg module provides a way to connect the loaded modules with your build system by setting environment variables. setuptools: setuptools/63.4.0-Python-3.10.4 Setuptools is a fully-featured, actively-maintained, and stable library designed to facilitate packaging Python projects. sextractor: sextractor/2.25.0 SExtractor is a program that builds a catalogue of objects from an astronomical image. Although it is particularly oriented towards reduction of large scale galaxy-survey data, it can perform reasonably well on moderately crowded star fields. shovill: shovill/1.1.0 Faster SPAdes assembly of Illumina reads showq: showq/0.15 sickle: sickle/1.33 Windowed Adaptive Trimming for fastq files using quality slow5tools: slow5tools/0.4.0 slow5tools is a toolkit for converting (FAST5 <-> SLOW5), compressing, viewing, indexing and manipulating data in SLOW5 format. slurm: slurm/latest smithwaterman: smithwaterman/20160702 smith-waterman-gotoh alignment algorithm. snakemake: snakemake/7.22.0 The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. snappy: snappy/1.1.9 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: snippy/4.6.0 Rapid haploid variant calling and core genome alignment snp-sites: snp-sites/2.5.1 Finds SNP sites from a multi-FASTA alignment file. snpEff: snpEff/5.0e-Java-11 SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). snptest: snptest/2.5.6 SNPTEST is a program for the analysis of single SNP association in genome-wide studies. sparsehash: sparsehash/2.0.4 An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. spartan: spartan/rhel9, spartan/2016-03-parallel statsmodels: statsmodels/0.13.1 Statsmodels is a Python module that allows users to explore data, estimate statistical models, and perform statistical tests. tabix: tabix/0.2.6 Generic indexer for TAB-delimited genome position files tabixpp: tabixpp/1.1.0 C++ wrapper to tabix indexer tbb: tbb/2021.5.0 Intel(R) Threading Building Blocks (Intel(R) TBB) lets you easily write parallel C++ programs that take full advantage of multicore performance, that are portable, composable and have future-proof scalability. tbl2asn: tbl2asn/20220427-linux64 Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank tcsh: tcsh/6.24.01 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. tensorboard: tensorboard/2.10.0 TensorBoard is a suite of web applications for inspecting and understanding your TensorFlow runs and graphs. texinfo: texinfo/7.0.2 Texinfo is the official documentation format of the GNU project. texlive: texlive/20230313 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. torchvision: torchvision/0.13.1 Datasets, Transforms and Models specific to Computer Vision tqdm: tqdm/4.64.0 A fast, extensible progress bar for Python and CLI trimAl: trimAl/1.4.1 EVB, FEP and LIE simulator. unimelb-mf-clients: unimelb-mf-clients/current unimelb-mf-clients is a collection of command-line tools to transfer data to/from Mediaflux, the data management platform operated by Research Computing Services utf8proc: utf8proc/2.7.0 utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. util-linux: util-linux/2.38 Set of Linux utilities vbz_compression: vbz_compression/1.0.2 VBZ compression HDF5 plugin for nanopolish vcflib: vcflib/1.0.3 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. versioneer: versioneer/0.28-Python-3.10.4 Easy VCS-based management of project version strings. vt: vt/0.57721 A tool set for short variant discovery in genetic sequence data. wget: wget/1.21.3 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. wgsim: wgsim/20111017 Wgsim is a small tool for simulating sequence reads from a reference genome. x264: x264/20220620 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: x265/3.5 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. xorg-macros: xorg-macros/1.19.3 X.org macros utilities. xprop: xprop/1.2.5 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: xproto/7.0.31 X protocol and ancillary headers xtb: xtb/6.5.1 xtb - An extended tight-binding semi-empirical program package. xxd: xxd/8.2.4220 xxd is part of the VIM package and this will only install xxd, not vim! xxd converts to/from hexdumps of binary files. yaml-cpp: yaml-cpp/0.7.0 yaml-cpp is a YAML parser and emitter in C++ matching the YAML 1.2 spec zlib: zlib/1.2.12, zlib/1.2.13 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: zstd/1.5.2 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. -------------------------------------------------------------------------------------------------------------------------------- To learn more about a package execute: $ module spider Foo where "Foo" is the name of a module. To find detailed information about a particular package you must specify the version if there is more than one version: $ module spider Foo/11.1 --------------------------------------------------------------------------------------------------------------------------------