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 |
|---|---|---|
| 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 | antiSMASH is a docker container preloaded with Fermitools, the HEASARC FTOOLS, and python libraries. The module makes antiSMASH release 23.05.19.0 available. The list of preloaded software is as follows: | 23.05.19.0 |
| 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 |
| 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 bbtools bundle packages version 39.01. | 39.01 |
| 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 bcftools bundle packages version 1.17. | 1.17 |
| BEAST and BEAST2 | BEAST and BEAST 2 are cross-platform programs for Bayesian phylogenetic analysis of molecular sequences. The beast bundle packages version 1.10.4 of BEAST and version 2.6.3 of BEAST 2. | 2.6.3 |
| 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 |
| BLAST | BLAST, Basic Local Alignment Search Tool, can be used for sequence similarity searching. The blast bundle packages NCBI Blast version 2.14.0. | 2.14.0 |
| 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 |
| 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 |
| 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 avaialable 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 |
| CoolProp | CoolProp is a thermophysical property database and can be used for fluid dynamic computations.The bundle packages the following software: | 6.4.3 |
| 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 15.13.1. | 15.13.1 |
| 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 diting bundle packages version 0.9. | 0.9 |
| 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 |
| 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 |
| fatsp | 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. The module makes Fermibottle release 23.03.10.0 available. The list of preloaded software is as follows: | 2.2.0 |
| 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 |
| 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 |
| Geneious Prime | Geneious Prime is a comprehensive suite of molecular biology and sequence analysis tools. The bundle packages version 2023.2.1. | 2023.2.1 |
| 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 |
| 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 |
| 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 |
| IVA | IVA is a de novo assembler designed to assemble virus genomes that have no repeat sequences. The iva bundle packages version 1.0.8. | 1.0.8 |
| 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 |
| 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 |
| 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 metabat bundle packages version 2.15. | 2.15 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| OrthoFinder | OrthoFinder is a platform for comparative genomics. The orthofinder 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 |
| 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 |
| 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 |
| GRRG - Grid Related Research Group | The grrg bundle is used for data and network analyis of electrical grids. The module makes variants with Python 3.9 and 3.10 available. | unknown |
| QIIME2 | The QIIME 2 bundle is used for next-generation microbiome analysis. | 2023.2.0 2023.5.1 |
| QualiMap | QualiMap facilitates the quality control of alignment sequencing data and its derivatives like feature counts. | unknown |
| RAxML | RAxML, Randomized Axelerated Maximum Likelihood, can be used for maximum likelihood-based phylogenetic analyses. The raxml bundle packages version 8.2.12. | 8.2.12 |
| Remmina | Remmina s a Remote Desktop Client that supports SSH, VNC and RDP. The bundle packages version 1.4.31. | 1.4.31 |
| Fermibottle | Fermibottle is a docker container preloaded with Fermitools, the HEASARC FTOOLS, and python libraries. The module makes Fermibottle release 23.05.19.0 available. The list of preloaded software is as follows: | 23.05.19.0 |
| Roary | Roary is a high speed stand alone pan genome pipeline. The roary 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 rtgtools 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 |
| MAFFT | Salmon is used to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. The salmon bundle packages version 1.10.1. | 1.10.1 |
| 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 seqkit bundle packages version 2.5.0. | 2.5.0 |
| sickle | sickle is a windowed adaptive trimming tool for FASTQ files using quality. The sickle bundle packages version 1.33. | 1.33 |
| 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 |
| SPAdes | SPAdes, Saint-Petersburg genome assembler, is an assembly toolkit containing various assembly pipelines. The spades bundle packages version 3.15.5. | 3.15.5 |
| 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 3.0.5. | 3.0.5 |
| Stress-NG | The stressng bundle is used for benchmarking and stress testing hardware. | unknown |
| StringTie | StringTie can be used for transcript assembly and quantification for RNA-Seq. The stringtie bundle packages version 2.2.1. | 2.2.1 |
| TaxonKit | TaxonKit is a practical and efficient NCBI taxonomy toolkit. The taxonkit bundle packages version 0.15.0. | 0.15.0 |
| 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 |
| 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 |
| Remmina | Remmina s a Remote Desktop Client that supports SSH, VNC and RDP. The bundle packages version 1.4.31. | 1.4.31 1.5.3 |
| Unicycler | Unicycler is an assembly pipeline for bacterial genomes. The unicycler bundle packages version 0.5.0. | 0.5.0 |
| 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 |
| TempEst | TempEst is used to investigate the temporal signal and 'clocklikeness' of molecular phylogenies. The version packaged is 1.5.3. | 1.5.3 |
| Wine | Wine is a compatibility layer capable of running Windows applications on Linux. The bundle packages version 8.0.1. | 8.0.1 |