eRN Software¶
The following is a list of software the HPC and eRN team maintains. Note that not all approved/maintained software may be listed here. This list will be updated occasionally, and we ask for your patience in this regard.
| Software Name | Description | Version |
|---|---|---|
| Utilities | 1 |
|
| ABySS | ABySS is a de novo paired-end sequence assembler that is designed for short reads. The abyss bundle packages version 2.3.6. | 2.3.6 |
| antiSMASH - the antibiotics and Secondary Metabolite Analysis SHell | antiSMASH is able to identify the gene clusters encoding secondary metabolites. The module makes antiSMASH release 7.1.0 available. | 7.1.0 |
| AquaCrop | The aquacrop bundle is a python implementation of the crop-water model AquaCrop. The bundle packages version 2.2.3. | 2.2.3 |
| ARAGORN | ARAGORN is used to detect tRNA genes and tmRNA genes in nucleotide sequences. The aragorn bundle packages version 1.2.41. | 1.2.41 |
| Artemis | Artemis is a DNA sequence viewer and annotation tool that allows visualisation of sequence features and the results of analyses within the context of the sequence, and its six-frame translation. The artemis bundle packages version 18.2.0. | 18.2.0 |
| Astropy and PyAstronomy | Astropy and PyAstronomy are packages for Astronomy in Python. Astropy version 5.3.2, and PyAstronomy version 0.18.0 is packaged. | 5.3.2 |
| AUGUSTUS | AUGUSTUS predicts genes in eukaryotic genomic sequences. The augustus bundle packages version 3.5.0. | 3.5.0 |
| Authoring | The authoring bundle is a collection of Latex, Tex, PDF, DOCX, Markdown and text files editing and viewing software. The bundle includes the following software: | unknown |
| BamTools | BamTools provides a toolkit for handling BAM files. The bamtools bundle packages version 2.5.2. | 2.5.2 |
| Bandage | Bandage is used to visualise de novo assembly graphs. The bandage bundle packages version 0.8.1. | 0.8.1 |
| Barrnap | Barrnap predicts the location of ribosomal RNA genes in genomes. The barrnap bundle packages version 0.9. | 0.9 |
| BBTools | BBTools is a suite of tools designed for the analysis of DNA and RNA sequence data. The bundle packages version 39.19. | 39.01 39.19 |
| BCALM | BCALM constructs the compacted de Bruijn graph from sequencing data. The bcalm bundle packages version 2.2.3. | 2.2.3 |
| BCFtools | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. The bundle packages version 1.21. | 1.17 1.21 |
| BEAST and BEAST2 | BEAST and BEAST 2 are cross-platform programs for Bayesian phylogenetic analysis of molecular sequences. The beast bundle packages version 10.5.0-beta5 of BEAST and version 2.7.7 of BEAST 2. | 2.6.3 2.7.7 |
| Bedtools | The bedtools utilities are a swiss-army knife of tools for a wide-range of genomics analysis tasks. The bedtools bundle packages version 2.31.0. | 2.31.0 |
| BiG-SCAPE: Biosynthetic Gene Similarity Clustering and Prospecting Engine | BiG-SCAPE constructs sequence similarity networks of Biosynthetic Gene Clusters and groups them into Gene Cluster Families. The bigscape bundle packages version 1.1.8. The PFAM database was downloaded, extracted, and processed with the following commands: bash wget http://mirror.ufs.ac.za/datasets/pfam/current_release/Pfam-A.hmm.gz gunzip Pfam-A.hmm.gz hmmpress Pfam-A.hmm |
1.1.8 |
| Bismark Bisulfite Mapper | Bismark is a set of tools for the analysis of Bisulfite-Seq (BS-Seq) data. The bundle packages Bismark version 0.24.2. | 3.0.0 |
| BLAST | The Basic Local Alignment Search Tool can be used for sequence similarity searching. The bundle packages NCBI BLAST version 2.15.0. | 2.14.0 2.15.0 |
| BLUPF90 | The BLUPF90 family of programs is a collection of software for mixed model computations in animal breeding. The version packaged is 20240516. | 20240516 |
| Bowtie | Bowtie and Bowtie 2 are tools for aligning sequencing reads to long reference sequences. The bowtie bundle has two variants one for version 1.3.1 and one for version 2.5.1. | 2.5.1 |
| BUSCO | BUSCO can be used to assess genome assembly and annotation completeness. The busco bundle packages version 5.4.7. | 5.4.7 |
| BUSCO Phylogenomics | BUSCO Phylogenomics is a pipeline to construct species phylogenies using BUSCO Phylogenomics proteins. The bundle packages version 20240904. | 20240904 |
| BWA | BWA, Burrow-Wheeler Aligner, is used for short-read alignment. The bwa bundle packages version 0.7.17. | 0.7.17 |
| Canu | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing. The canu bundle packages version 2.2. | 2.2 |
| CASA | CASA, the Common Astronomy Software Applications package, is used for data processing of radio telescopes. The version packaged is 6.5.5. | 6.5.5 |
| CD-HIT | CD-HIT is used for clustering biological sequences to reduce sequence redundancy and improve the performance of other sequence analyses. The cdhit bundle packages version 4.8.1. | 4.8.1 |
| CheckM | CheckM is a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. The checkmgenome bundle packages version 1.2.2. | 1.2.2 |
| chopper | chopper is a Rust implementation of NanoFilt+NanoLyse, and is intended for long read sequencing such as PacBio or ONT, to filter and trim FASTQ files. chopper version 0.8.0 is packaged. | 0.8.0 |
| Chromium | Chromium is an open source browser. The bundle packages version 134.0.6998.88. | 127.0.6533.88 134.0.6998.88 |
| CIAO - Chandra Interactive Analysis of Observations | The ciao bundle contains the following versions of the listed software. | 4.15.1 |
| CLC Genomics Workbench | CLC Genomics Workbench is a complete toolkit for genomics, transcriptomics, epigenomics, metagenomic. The bundle packages version 24.0. | 23.0.5 24.0 |
| Clustal Omega | Clustal Omega is used to align multiple amino acid or nucleotide sequences. The clustalo bundle packages version 1.2.4. | 1.2.4 |
| Clustal W | Clustal W is used to align multiple amino acid or nucleotide sequences. The clustalw bundle packages version 2.1. | 2.1 |
| CONCOCT | CONCOCT is used for unsupervised binning of metagenomic contigs by using nucleotide composition. The concoct bundle packages version 1.1.0. | 1.1.0 |
| Anaconda | The conda bundle is used to quickly create bundles that package software available in the Anaconda repositories. The module makes variants using Rocky Linux and Fedora as operating systems available. Python 3.11 and 3.12 are supported. | 23.1.0 24.1.2 |
| CoolProp | CoolProp is a thermophysical property database and can be used for fluid dynamic computations.The bundle packages the following software: | 6.4.3 |
| CSpell | CSpell is a spell checker for code. Support for the following languages and document formats are included: shell, Docker, Latex, Markdown, Make, bash, SQL, Julia, Python, and R. In addition dictionaries are included for: data science, file types, fonts, git, software terms, scientific terms, and GIS. The bundle packages version 8.18.1. | 8.18.1 |
| Cufflinks | Cufflinks assembles transcripts, estimates their abundances, and tests for differential expression and regulation in RNA-Seq samples. The cufflinks bundle packages version 2.2.1. | 2.2.1 |
| NCBI Datasets | NCBI Datasets CLI allows you to find and download sequence, annotation, and metadata for genes and genomes. The datasetscli bundle packages NCBI Datasets CLI version 16.20.0. | 15.13.1 16.20.0 |
| Debian | Debian is a distribution of Linux. The module makes variants of Debian Bookworm and Trixie, with developer tools preinstalled, and without available. | 12 |
| DIAMOND | DIAMOND is a sequence aligner for protein and translated DNA searches. The diamond bundle packages version 2.1.6. | 2.1.6 |
| DiTing | DiTing recognizes biogeochemical cycles from environmental omic data accurately and efficiently. The bundle packages version 0.9. | 0.9 |
| Dorado | Dorado is an easy-to-use basecaller for Oxford Nanopore reads. The bundle packages version 0.8.3. | 0.7.3 0.8.3 |
| ea-utils | Command-line tools for processing biological sequencing data, for example: Barcode demultiplexing, adapter trimming, etc. The eautils bundle packages version 1.1.2.537. | 1.1.2.537 |
| EggNOG-mapper (Hypothesis Testing using Phylogenies) | EggNOG-mapper is a tool for fast functional annotation of novel sequences. The bundle packages version 2.1.12. | 2.1.12 |
| Entrez Direct | Entrez Direct provides access to the NCBI's suite of interconnected databases. The bundle packages Entrez Direct version 22.1. | 22.1 |
| Anaconda | The conda bundle is used to quickly create bundles that package software available in the Anaconda repositories. The module makes variants using Rocky Linux and Fedora as operating systems available. Python 3.9 and 3.10 are supported. | 23.1.0 |
| EukRep | EukRep is used to classify of Eukaryotic and Prokaryotic sequences from metagenomic datasets. The eukrep bundle packages version 0.6.7. | 0.6.7 |
| fastp | fastp provides all-in-one preprocessing for FastQ files. The fastp bundle packages version 0.23.2. | 0.23.2 |
| FastQC | FastQC is a quality control tool for high throughput sequence data. The fastqc bundle packages version 0.12.1. | 0.12.1 |
| FastTree | FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. The fasttree bundle packages version 2.1.11. | 2.1.11 |
| Fedora | Fedora is a distribution of Linux. The module makes variants of Fedora 37 with developer tools preinstalled and without available. | 37 |
| FermiBottle | FermiBottle is a docker container preloaded with Fermitools, the HEASARC FTOOLS, and python libraries. Release 24.05.14.1 is packaged. The list of preloaded software is as follows: | 2.2.0 24.05.14.1 |
| Fermi Science Tools | Fermi Science Tools is used to access, analyse, and visualize data from the Fermi Gamma-ray Space Telescope. A newer release of the software is available in the fermibottle bundle. The legacy version made available in this bundle is 11r5p3. | 11r5p3 |
| FigTree | FigTree is a graphical viewer of phylogenetic trees. The figtree bundle packages version 1.4.4. | 1.4.4 |
| Flye | Flye is a de novo assembler for single-molecule sequencing reads. The flye bundle packages version 2.9.2. | 2.9.2 |
| FragGeneScan | FragGeneScan finds fragmented genes in short reads. It can also be used to predict prokaryotic genes in incomplete assemblies or complete genomes. The fraggenescan bundle packages version 1.31. | 1.31 |
| freebayes | freebayes is a Bayesian genetic variant detector. The freebayes bundle packages version 1.3.6. | 1.3.6 |
| Gammapy | Gammapy is a package for gamma-ray astronomy and is widely used in the analysis of existing gamma-ray instruments, such as MAGIC, VERITAS and HAWC. Gammapy version 1.3 is packaged. | 1.3 |
| GATE | GATE supports simulation of Emission Tomography, Optical Imaging, Radiotherapy experiments. Dose calculations in radiation therapy and brachytherapy can also be done. GATE version 10.0.1 is packaged. | 10.0.1 |
| Genome Analysis Toolkit (GATK) | The Genome Analysis Toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. The gatk bundle packages version 4.4.0.0. | 4.4.0.0 |
| Gblocks | Gblocks eliminates poorly aligned positions and divergent regions of an alignment of DNA or protein sequences. The gblocks bundle packages version 0.91b. | 0.91b |
| Geany | Geany is a lightweight programmer's text editor that has built-in support for more than 50 programming languages. The bundle packages version 2.0. | 2.0 |
| Geneious Prime | Geneious Prime is a comprehensive suite of molecular biology and sequence analysis tools. The bundle packages version 2024.0.5. | 2023.2.1 2024.0.5 |
| Gephi | Gephi is software that cab be used to visualise and explore all kinds of graphs and networks. The version packaged is 0.10.1. | 0.10.1 |
| Git | Git is a distributed version control system designed to handle everything from small to large projects with speed and efficiency. The bundle packages version 2.46.2. | 2.46.2 |
| GrADS | GrADS, Grid Analysis and Display System, is used to access, manipulate and visualize geophysical data. The latest and only version available, on the eRN, is 2.2.1. | 2.2.1 |
| GRRG - Grid Related Research Group | The grrg bundle is used for data and network analysis of electrical grids. The module makes variants with Python 3.9 and 3.10 available. | unknown |
| Gubbins | Gubbins 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. The gubbins bundle packages version 3.3. | 3.3 |
| Guppy | Guppy is a data toolkit for Oxford Nanopore Technologies' sequencing platforms. The bundle packages version 6.5.7. | 6.5.7 |
| HDF5 Tools | HDF5 Tools, a collection of tools to view and manipulate h5 files. The hdf5tools bundle packages the following software: | 1.14.3 |
| Hifiasm | Hifiasm is a fast haplotype-resolved de novo assembler for PacBio HiFi reads. The hifiasm bundle packages version 0.19.6. | 0.19.6 |
| HISAT2 | HISAT2 is an alignment program for mapping NGS reads against a reference genome. The hisat2 bundle packages version 2.2.1. | 2.2.1 |
| HMMER | HMMER provides tools for making probabilistic models of protein and DNA sequence domain families. The hmmer bundle packages version 3.3.2. | 3.3.2 |
| Canu | Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing. The canu bundle packages version 2.2. | 2.2 |
| Hybracter | Hybracter is an automated long-read first bacterial genome assembly tool. The module makes Hybracter release 0.11.2 available. | 0.11.2 |
| hylite | An open source python toolbox for hyperspectral data preprocessing, correction, projection and analysis. The bundle packages version 1.31 of hylite and version 0.75 of hycore. |
1.31 |
| HyPhy (Hypothesis Testing using Phylogenies) | HyPhy is a software package for comparative sequence analysis using stochastic evolutionary models. The bundle packages version 2.5.62. | 2.5.62 |
| IDBA | IDBA is the basic iterative de Bruijn graph assembler for second-generation sequencing reads. The idba bundle packages version 1.1.3. | 1.1.3 |
| IGV | The Integrative Genomics Viewer (IGV) is a tool for the visual exploration of genomic data. The igv bundle packages version 2.13.2. | 2.13.2 |
| IQ-TREE | IQ-TREE can be used for phylogenomic inference. The iqtree bundle packages version 2.2.2.3. | 2.2.2.3 |
| IRAF | IRAF can be used for the reduction and analysis of astronomical data. | 20231103 |
| IVA | IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences. The bundle packages version 1.0.8. | 1.0.8 |
| Jalview | Jalview can be used for multiple sequence alignment editing, visualisation and analysis. Jalview version 2.11.4.1 is packaged. | 2.11.4.1 |
| Julia | Julia, is a programming language often used in computational science. | 1.8.5 1.9.1 |
| Kaiju | Kaiju is used for the taxonomic classification of high-throughput sequencing reads. The kaiju bundle packages version 1.9.2. | 1.9.2 |
| Kraken 2 | Kraken 2 is a taxonomic classification system using exact k-mer matches to achieve high accuracy and fast classification speeds. The kraken bundle packages the following software: | 2.1.3 |
| Krona Tools | Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. The krona bundle packages version 2.8.1. | 2.8.1 |
| Ksnip | Ksnip is a screenshot tool that provides many annotation features for your screenshots. The bundle packages version 1.10.1. | 1.10.1 |
| Lambda: the Local Aligner for Massive Biological DatA | Lambda is a local aligner that can be used for protein, nucleotide, and bisulfite searches. Some degree of compatibility with NCBI BLAST is offered, but with improved speed. The lambda bundle packages Lambda version 3.0.0. | 3.0.0 |
| Latex | The bundle packages a collection of Tex editing and processing software. The bundle includes the following software: Two variants of the bundle are available: basic and full. The default variant is basic. If storage is a concern, then always test with the basic variant first as it requires much less space. | 2023.20240207-1 |
| LibreOffice | LibreOffice is a private, free and open source office suite. It's compatible with Microsoft Office/365 files. The bundle packages version 24.2.7.2. | 24.2.7.2 |
| LoFreq | LoFreq is a variant-caller for inferring SNVs and indels from next-generation sequencing data. The lofreq bundle packages version 2.1.5. | 2.1.5 |
| MAFFT | MAFFT is used to align multiple amino acid or nucleotide sequences. The mafft bundle packages version 7.520. | 7.520 |
| markdownlint-cli2 | markdownlint-cli2 is a fast, flexible, configuration-based command-line interface for linting Markdown and CommonMark files. The bundle packages version 0.17.2. | 0.17.2 |
| MARPLE Diagnostics | Pipeline for analysis of stem rust and yellow rust reads. The bundle packages version 1.3.2. | 1.17 |
| Medaka | Medaka creates consensus sequences and variant calls from Nanopore sequencing data. The bundle packages version 2.0.1. | 2.0.1 |
| MEGA | MEGA is a program for conducting statistical analysis of molecular evolution and for constructing phylogenetic trees. The mega bundle packages version 11.0.13. | 11.0.13 |
| MEGAHIT | MEGAHIT is an NGS assembler. The megahit bundle packages version 1.2.9. | 1.2.9 |
| MetaBAT | MetaBAT is a statistical framework for reconstructing genomes from metagenomic data. The bundle packages version 2.17. | 2.15 2.17 |
| MetaPhlAn | MetaPhlAn is a tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data with species level resolution. The metaphlan bundle packages version 4.0.6. | 4.0.6 |
| Metview | Metview is an application designed to be a complete working environment for both the operational and research meteorologist. The metview bundle packages version 5.19.1. | 5.19.1 |
| MicaSense | The bundle provides a development environment for use with the MicaSense RedEdge and Altum image processing tutorials. The yaml conda environment file was retrieved in June 2024. | 16.20.0 |
| Minimap2 | Minimap2 is a sequence alignment program that aligns DNA or mRNA sequences against a large reference database. The minimap2 bundle packages version 2.26. | 2.26 |
| ModelTest-NG | ModelTest-NG can be used to select the best-fit model of evolution for DNA and protein alignments. The modeltestng bundle packages version 0.1.7. | 0.1.7 |
| MrBayes | MrBayes is used for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. The mrbayes bundle packages version 3.2.7. | 3.2.7 |
| MultiQC | MultiQC aggregates results from bioinformatics analyses across many samples into a single report. The multiqc bundle packages version 1.14. | 1.14 |
| Muscle | Muscle is used to align multiple amino acid or nucleotide sequences. The muscle bundle packages version 5.1. | 5.1 |
| NanoFilt | NanoFilt can be used to filter on quality and/or read length, and optional trimming after passing filters. NanoFilt version 2.8.0 is packaged, however, NanoFilt does not receive any updates, please consider using chopper. | 2.8.0 |
| Nextclade | Nextclade is used for viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement. The nextclade bundle packages version 2.14.0. | 2.14.0 |
| Nextflow | Nextflow enables scalable and reproducible scientific workflows. The bundle packages version 24.04.4. | 24.04.4 |
| nf-core | nf-core is a community effort to collect a curated set of analysis pipelines built using Nextflow. The bundle packages the dependencies required by nf-core, see the table below for the versions of the included dependencies. | 1.3.23 |
| nnU-Net | nnU-Net is a semantic segmentation method that automatically adapts to a given dataset. Two module variants are available: one with CUDA 12.4, and one for CPU only. The bundle packages version 2.6.0. | 2.6.0 |
| Node.js | Node.js® is a JavaScript runtime environment that lets developers create servers, web apps, command line tools and scripts. The bundle packages version 22.14.0. | 22.14.0 |
| GNU Octave | GNU Octave has a powerful mathematics-oriented syntax with built-in 2D/3D plotting and visualization tools It provides a convenient command line interface for solving linear and nonlinear problems numerically, and for performing other numerical experiments using a language that is mostly compatible with Matlab. The octave bundle packages version 8.3.0. | 8.3.0 |
| oneAPI | The latest Intel platforms using an open, standards-based programming model that delivers increased performance for HPC applications and hardware choice across CPU, GPU, and other accelerators. Two of the toolkits are provided as module variants, namely: base and hpc. The version packaged is 2025.0.1. |
2025.0.1 |
| ORF finder | ORF finder searches for open reading frames (ORFs) in DNA sequences. The program returns the range of each ORF, along with its protein translation. The bundle packages version 0.4.3. | 0.4.3 |
| OrthoFinder | OrthoFinder is a platform for comparative genomics. The bundle packages version 2.5.5. | 2.5.5 |
| PEAR - Paired-End reAd mergeR | PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. The pear bundle packages version 0.9.6. | 0.9.6 |
| PhyML | PhyML is a phylogeny software based on the maximum-likelihood principle. The phyml bundle packages version 3.3.20211231. | 3.3.20211231 |
| Picard | Picard is a set of tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF. The picard bundle packages version 3.1.0. | 3.1.0 |
| Pilon | Pilon is a tool which can be used to: automatically improve draft assemblies, and find variation among strains. The bundle packages version 1.24. | 1.24 |
| PLINK | PLINK is a whole genome association analysis toolset. The plink bundle has three variants one for version 1.07, one for version 1.90b6.21, and one for version 2.00a3.7. | 2.00a3.7 |
| Anaconda | The conda bundle is used to quickly create bundles that package software available in the Anaconda repositories. The module makes variants using Rocky Linux and Fedora as operating systems available. Python 3.9 and 3.10 are supported. | unknown |
| PRANK | PRANK is a probabilistic multiple alignment program for DNA, codon, and amino-acid sequences. PRANK version 170427 is packaged. | 170427 |
| Prettier | Prettier is an opinionated code formatter for: JavaScript, JSX, Angular, Vue, Flow, TypeScript, CSS, Less, SCSS, HTML, Ember/Handlebars, JSON, GraphQL, Markdown, and YAML. The bundle packages version 3.5.3. | 3.5.3 |
| Prokka | Prokka is a software tool to annotate bacterial, archaeal and viral genomes. The prokka bundle packages version 1.14.6. | 1.14.6 |
| Purge_Dups | Purge_Dups can be used to purge haplotigs and overlaps in an assembly based on read depth. The purgedups bundle packages version 1.2.6. | 1.2.6 |
| PyMLST - A Python Mlst Local Search Tool | PyMLST is used to perform core or whole genome Multilocus Sequence Typing. The bundle packages the dependencies required by PyMLST, see the table below for the versions of the included dependencies. | 2.1.3 |
| PyMOL | PyMOL is a molecular visualization system. The pymol bundle packages version 2.5.0. | 2.5.0 |
| PySCF | A variety of electronic structure methods are implemented by PySCF. The module makes variants with Python 3.9 and 3.10 available. | 2.6.2 |
| QGIS | QGIS is a full-featured, user-friendly, geographic information system (GIS). The module makes variants with version 3.32 and 3.34 available. | 3.34 |
| QIIME 2 | The QIIME 2 bundle is used for next-generation microbiome analysis. The bundle packages version 2024.10. Four distributions are packaged: tiny, amplicon, metagenome, and pathogenome. | 2023.2.0 2023.5.1 2024.10 2024.5 |
| QualiMap | QualiMap facilitates the quality control of alignment sequencing data and its derivatives like feature counts. The qualimap bundle packages version 2.2.2d. | 2.2.2d |
| WOMBAT | WOMBAT is a program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML). | 20231103 |
| QUAST - Quality Assessment Tool for Genome Assemblies | QUAST evaluates genome assemblies by computing various metrics. The bundle packages version 5.2.0. | 5.2.0 |
| RagTag | RagTag is a set of tools for fast and flexible genome assembly, scaffolding, and improvement. The bundle packages version 2.1.0. | 2.1.0 |
| RAxML | RAxML, Randomized Axelerated Maximum Likelihood, can be used for maximum likelihood-based phylogenetic analyses. The bundle packages version 8.2.13. | 8.2.12 8.2.13 |
| RELION (REgularised LIkelihood OptimisatioN) | RELION employs an empirical Bayesian approach for electron cryo-microscopy (cryo-EM) structure determination. The bundle packages version 4.0.2. | 20231103 |
| Remmina | Remmina s a Remote Desktop Client that supports SSH, VNC and RDP. The bundle packages version 1.4.31. | 1.4.31 |
| RepeatMasker | RepeatMasker screens DNA sequences for interspersed repeats and low complexity DNA sequences. The bundle packages version 4.1.7p1. | 4.1.7p1 |
| rhyolite-MELTS | rhyolite-MELTS can be used for thermodynamic modeling of phase equilibria in magmatic systems. The bundle packages rhyolite-MELTS versions 1.0.2, 1.1.0, and 1.2.0; and pMELTS version 5.6.1. | 1.2.0 |
| Roary | Roary is a high speed stand alone pan genome pipeline. The bundle packages version 3.13.0. | 3.13.0 |
| Rocky Linux | Rocky Linux is a distribution of Linux based on RHEL. The module makes variants of Rocky Linux 8 and 9, with and without developer tools preinstalled available. | 9 |
| Rstudio | Rstudio is an IDE for R a language used for statistical programming and data science. The bundle also includes R with some often used packages preinstalled. The following versions are installed: | 2023.03.0+386 2023.06.2+561 |
| RTG Tools | RTG Tools includes several useful utilities for dealing with VCF files and sequence data. The bundle packages version 3.12.1. | 3.12.1 |
| S3A - Scalable and Accurate Annotated Assembly | S3A is a gene-targeted assembler based on the Overlap-Layout Consensus paradigm to reconstruct coding regions from domain annotated metagenomic sequence reads. | unknown |
| SageMath | The sage, "System for Algebra and Geometry Experimentation", bundle can be used for algebra, combinatorics, graph theory, numerical analysis, number theory, calculus and statistics. The module makes variants with Python 3.9, with SageMath 9.7, and 3.10, with SageMath 9.8, available. | 9.8 |
| Salmon | Salmon is used to produce a highly accurate, transcript-level quantification estimates from RNA-seq data. The bundle packages version 1.10.3. | 1.10.1 1.10.3 |
| Samtools | The samtools bundle can be used to manipulate NGS data. Samtools version 1.17 is packaged. | 1.17 |
| SeqKit | SeqKit is a toolkit for FASTA/Q file manipulation. The bundle packages version 2.10.0. | 2.10.0 2.5.0 |
| SeqMonk | SeqMonk is used to visualise and analyse high throughput mapped sequence data. The bundle packages version 1.48.1. | 1.48.1 |
| sickle | sickle is a windowed adaptive trimming tool for FASTQ files using quality. The sickle bundle packages version 1.33. | 1.33 |
| SIMIND | SIMIND describes a standard clinical SPECT camera and can be modified for almost any type of calculation or measurement encountered in SPECT imaging. The bundle packages version 8.0. | 8.0 |
| SimPlot++ | Simplot++ produces publication-ready plots using 43 nucleotide and 20 amino acid distance models. Intergenic and intragenic recombination events can be identified using Phi, ?2, NSS and Proportion tests. The bundle packages version 1.3. | 1.3 |
| 3D Slicer | 3D Slicer is used for visualization, processing, segmentation, registration, and analysis of medical, biomedical, and other 3D images and meshes. The version packaged is 5.6.0. | 5.6.0 |
| Snippy | Snippy finds both substitutions (SNPs) and insertions/deletions (indels) between a haploid reference genome and your NGS sequence reads. The bundle packages version 4.6.0. | 4.6.0 |
| SPAdes | SPAdes, Saint-Petersburg genome assembler, is an assembly toolkit containing various assembly pipelines. The bundle packages version 4.1.0. | 3.15.5 4.1.0 |
| SRA Toolkit | The SRA Toolkit and SDK is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. The sratools bundle packages version 3.1.1. | 3.0.5 3.1.1 |
| STAR-CCM+ | STAR-CCM+ is a program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML). | 20231103 |
| Stress-NG | Stress-ng is used for benchmarking and stress testing hardware. The stressng bundle packages version 0.15.00. | 0.15.00 |
| StringTie | StringTie can be used for transcript assembly and quantification for RNA-Seq. The stringtie bundle packages version 2.2.1. | 2.2.1 |
| Rstudio | Rstudio is an IDE for R a language used for statistical programming and data science. The bundle also includes R with some often used packages preinstalled. The following versions are installed: | 2023.06.2+561 |
| TaxonKit | TaxonKit is a practical and efficient NCBI taxonomy toolkit. The bundle packages version 0.17.0. | 0.15.0 0.17.0 |
| TempEst | TempEst is used to investigate the temporal signal and 'clocklikeness' of molecular phylogenies. The version packaged is 1.5.3. | 1.5.3 |
| TopHat | TopHat is a fast splice junction mapper for RNA-Seq reads. The tophat bundle packages version 2.1.1. | 2.1.1 |
| Tracer | Tracer is used to visualise and analyse the MCMC trace files generated through Bayesian phylogenetic inference. The tracer bundle packages version 1.7.2. | 1.7.2 |
| Trans-ABySS | Trans-ABySS is a de novo RNAseq assembler using ABySS. The transabyss bundle packages version 2.0.1. | 2.0.1 |
| TransDecoder | TransDecoder identifies candidate coding regions within transcript sequences. The bundle packages version 5.7.1. | 5.7.1 |
| treePL | treePL is a phylogenetic penalized likelihood program. treePL version 2.6.3 is packaged. | 2.6.3 |
| Trim Galore | Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files. The trimgalore bundle packages version 0.6.10. | 0.6.10 |
| Trimmomatic | Trimmomatic is a flexible trimmer for Illumina Sequence Data. The trimmomatic bundle packages version 0.39. | 0.39 |
| Trinity | Trinity assembles transcript sequences from Illumina RNA-Seq data. The trinity bundle packages version 2.15. | 2.15 |
| TurboVNC | TurboVNC is an implementation of VNC that uses the Remote Frame Buffer protocol to remotely control another computer. The bundle packages version 3.1.2. | 3.1.2 |
| Ubuntu | Ubuntu is a distribution of Linux based on Debian. The module makes variants of Ubuntu 22.04 and 24.04, with developer tools preinstalled, and without available. | 9 |
| Unipro UGENE | Unipro UGENE is a unified bioinformatics toolkit that aims to assist novice molecular biologists The bundle packages version 51.0. | 51.0 |
| Unicycler | Unicycler is an assembly pipeline for bacterial genomes. The unicycler bundle packages version 0.5.0. | 0.5.0 |
| vcf2phylip | vcf2phylip converts SNPs in VCF format to PHYLIP, NEXUS, binary NEXUS, or FASTA alignments for phylogenetic analysis. The bundle packages version 2.9. | 2.9 |
| VCFtools | VCFtools provides easily accessible methods for working with complex genetic variation data in the form of VCF files. The vcftools bundle packages version 0.1.16. | 0.1.16 |
| Velvet | Velvet is a short read de novo assembler using de Bruijn graphs. The velvet bundle packages version 1.2.10. | 1.2.10 |
| GrADS | GrADS, Grid Analysis and Display System, is used to access, manipulate and visualize geophysical data. The latest and only version available, on the ERN, is 2.2.1. | 2.2.1 |
| Wine | Wine is a compatibility layer capable of running Windows applications on Linux. The bundle packages version 8.0.1. | 8.0.1 |
| WOMBAT | WOMBAT is a program to facilitate analyses fitting a linear, mixed model via restricted maximum likelihood (REML). | 20231103 |
| yamllint | yamllint is a linter for YAML files that checks for: syntax validity, key repetition, line lengths, trailing spaces, indentation, and so on. The bundle packages version 1.37.0. | 1.37.0 |