Biocluster Applications
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| Application | Installed Versions | Description |
|---|---|---|
| BamTools | 2.5.3-IGB-gcc-15.2.0 | BamTools provides both a programmers API and an end-users toolkit for handling BAM files. |
| BBMap | 39.59-IGB-gcc-15.2.0-Java-25.0.1 | BBMap short read aligner, and other bioinformatic tools. |
| BCFtools | 1.22-IGB-gcc-15.2.0 | BCFtools is a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart BCF. Includes https://github.com/freeseek plugins |
| BEDTools | 2.31.1-IGB-gcc-15.2.0 | 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. |
| biom-format | 2.1.17-IGB-gcc-15.2.0-Python-3.14.0 | The BIOM file format (canonically pronounced biome) is designed to be a general-useformat for representing biological sample by observation contingency tables. |
| BioPerl | 1.7.8-IGB-gcc-15.2.0 | Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. |
| Biopython | 1.86-IGB-gcc-15.2.0-Python-3.14.0 1.88-IGB-gcc-15.2.0-Python-3.14.0 |
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. |
| BLAST | 2.2.26 | 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+ | 2.17.0-IGB-gcc-15.2.0 | 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. |
| Bowtie2 | 2.5.4-IGB-gcc-15.2.0 | Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. |
| breseq | 0.40.3-IGB-gcc-15.2.0 | is a computational pipeline for the analysis of short-read re-sequencing data (e.g. Illumina, 454, IonTorrent, etc.). It uses reference-based alignment approaches to predict mutations in a sample relative to an already sequenced genome. |
| BWA | 0.7.19-IGB-gcc-15.2.0 | Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. |
| CD-HIT | 4.8.1-IGB-gcc-15.2.0 | CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. |
| cellranger | 9.0.0 | Cell Ranger is a set of analysis pipelines that process Chromium single cell 3 RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. |
| cellranger-arc | 2.0.2 | Cell Ranger ARC is a set of analysis pipelines that process Chromium Single Cell Multiome ATAC + Gene Expression sequencing data to generate a variety of analyses pertaining to gene expression, chromatin accessibility and their linkage. |
| cellranger-atac | 2.1.0 | Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. |
| Clustal-Omega | 1.2.4-IGB-gcc-15.2.0 | 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 |
| CNVkit | 0.9.14-IGB-gcc-15.2.0-Python-3.14.0 | A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing. |
| coniii | 4.0.2-IGB-gcc-15.2.0-Python-3.14.0 | ConIII is a Python package for solving maximum entropy problems with a focus on the pairwise maximum entropy model, also known as the inverse Ising problem. |
| coreutils | 9.9-IGB-gcc-15.2.0 | The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system.These are the core utilities which are expected to exist on every operating system. |
| CoverM | 0.8.0 | CoverM aims to be a configurable, easy to use and fast DNA read coverage and relative abundance calculator focused on metagenomics applications. |
| CUDA | 13.0.3 13.1.0 |
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. |
| cuDNN | 9.17.1.4-CUDA-13.1.0 | The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. |
| cutadapt | 5.2-IGB-gcc-15.2.0-Python-3.14.0 | Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. |
| deepTools | 3.5.6-IGB-gcc-15.2.0-Python-3.14.0 | deepTools addresses the challenge of handling the large amounts of data that are now routinely generated from DNA sequencing centers. deepTools contains useful modules to process the mapped reads data for multiple quality checks, creating normalized coverage files in standard bedGraph and bigWig file formats, that allow comparison between different files (for example, treatment and control). Finally, using such normalized and standardized files, deepTools can create many publication-ready visualizations to identify enrichments and for functional annotations of the genome. |
| DendroPy | 5.0.8-IGB-gcc-15.2.0-Python-3.14.0 | DendroPy is a Python library for phylogenetic computing. |
| DIAMOND | 2.1.16-IGB-gcc-15.2.0 | Accelerated BLAST compatible local sequence aligner |
| dorado | 2.1.2 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. |
| ds3_java_cli | 5.6.0 | Command line utilities for Bioarchive |
| EasyBuild | 5.4.0 | EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. |
| FastK | 1.2-IGB-gcc-15.2.0 | FastK is a k‑mer counter that is optimized for processing high quality DNA assembly data sets such as those produced with an Illumina instrument or a PacBio run in HiFi mode. For example it is about 2 times faster than KMC3 when counting 40-mers in a 50X HiFi data set. Its relative speedup decreases with increasing error rate or increasing values of k, but regardless is a general program that works for any DNA sequence data set and choice of k. It is further designed to handle data sets of arbitrarily large size, e.g. a 100X data set of a 32GB Axolotl genome (3.2Tbp) can be performed on a machine with just 12GB of memory provided it has ~6.5TB of disk space available. |
| fastp | 1.3.7-IGB-gcc-15.2.0 | A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. |
| FastQC | 0.12.1-Java-25.0.1 | FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. |
| FastTree | 2.2-IGB-gcc-15.2.0 | 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. |
| Filtlong | 0.3.1-IGB-gcc-15.2.0 | Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter. |
| Flye | 2.9.6-IGB-gcc-15.2.0-Python-3.14.0 | Flye is a de novo assembler for single molecule sequencing reads, such as those produced by PacBio and Oxford Nanopore Technologies. |
| GATK | 4.6.2.0-IGB-gcc-15.2.0-Java-25.0.1 | 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 | 15.2.0 | The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). |
| GDAL | 3.13.3-IGB-gcc-15.2.0 | 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. |
| gfatools | 0.5-IGB-gcc-15.2.0 | gfatools is a set of tools for manipulating sequence graphs in the GFA or the rGFA format. It has implemented parsing, subgraph and conversion to FASTA/BED. |
| gffread | 0.12.9-IGB-gcc-15.2.0 | The program gffread can be used to validate, filter, convert and perform various other operations on GFF files |
| gnuplot | 6.0.3-IGB-gcc-15.2.0 | Portable interactive, function plotting utility |
| GROMACS | 2026.4-IGB-gcc-15.2.0 | 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. |
| h5py | 3.16.0-IGB-gcc-15.2.0-Python-3.14.0 | a toolkit for working with nanopore sequencing data from Oxford Nanopore. |
| HDF5 | 1.14.6-IGB-gcc-15.2.0 2.1.1-IGB-gcc-15.2.0 |
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. |
| hifiasm | 0.25.0-IGB-gcc-15.2.0 | Hifiasm is a fast haplotype-resolved de novo assembler for PacBio Hifi reads. Unlike most existing assemblers, hifiasm starts from uncollapsed genome. Thus, it is able to keep the haplotype information as much as possible. |
| HISAT2 | 2.2.1-IGB-gcc-15.2.0 | HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). |
| HMMER | 3.4-IGB-gcc-15.2.0 | 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. |
| hmmlearn | 0.3.3-IGB-gcc-15.2.0-Python-3.14.0 | hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models |
| HTSlib | 1.22-IGB-gcc-15.2.0 | A C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix |
| IGB-gcc | 15.2.0 | GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. |
| Java | 21.0.8 25.0.1 |
Java Platform, Standard Edition (Java SE) lets you develop and deployJava applications on desktops and servers. |
| Jellyfish | 2.3.1-IGB-gcc-15.2.0 | Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. A k-mer is a substring of length k, and counting the occurrences of all such substrings is a central step in many analyses of DNA sequence. |
| Kraken2 | 2.17.1-IGB-gcc-15.2.0 | 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. |
| MACS3 | 3.0.5-IGB-gcc-15.2.0-Python-3.14.0 | A powerful tool for identifying transcription factor binding sites. |
| MariaDB | 12.1.2-IGB-gcc-15.2.0 | MariaDB An enhanced, drop-in replacement for MySQL. |
| MATLAB | 2017a | 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. |
| MEME | 5.5.9-IGB-gcc-15.2.0 | 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. |
| MetaEuk | 7-IGB-gcc-15.2.0 | MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. MetaEuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to recover optimal exons sets. |
| metaphlan | 4.2.5-IGB-gcc-15.2.0-Python-3.14.0 | MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea and Eukaryotes) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. |
| MIJAMP | 20250922-IGB-gcc-15.2.0 | Detecting bacterial methylation motifs is of interest to synthetic biologists working with newly domesticated strains, as cells use these methylation patterns to determine which DNA molecules are "theirs" and which are "alien", examples of that latter including viral genomes and plasmids. |
| Miniconda3 | 26.7.1 | 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. |
| minimap2 | 2.30-IGB-gcc-15.2.0 | Minimap2 is a versatile sequence alignment program that aligns DNA or mRNA sequences against a large reference database. |
| MMseqs2 | 18-8cc5c-IGB-gcc-15.2.0 | MMseqs2 (Many-against-Many sequence searching) is a software suite to search and cluster huge protein and nucleotide sequence sets. |
| modkit | 0.6.4 | A bioinformatics tool for working with modified bases from Oxford Nanopore. Specifically for quickly converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics. |
| MultiQC | 1.35-IGB-gcc-15.2.0-Python-3.14.0 | MultiQC searches a given directory for analysis logs and compiles a HTML report. Its a general use tool, perfect for summarising the output from numerous bioinformatics tools. |
| nanopolish | 0.14.0-IGB-gcc-15.2.0 | Software package for signal-level analysis of Oxford Nanopore sequencing data. |
| netCDF | 4.9.3-IGB-gcc-15.2.0 | 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-Fortran | 4.6.3-IGB-gcc-15.2.0 | 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. |
| nextflow | 24.04.6-Java-21.0.8 25.10.2-Java-25.0.1 |
Nextflow enables scalable and reproducible scientific workflows using software containers. It allows the adaptation of pipelines written in the most common scripting languages. |
| numba | 0.67.0-IGB-gcc-15.2.0-Python-3.14.0 | Numba is an Open Source NumPy-aware optimizing compiler forPython sponsored by Continuum Analytics, Inc. It uses the remarkable LLVMcompiler infrastructure to compile Python syntax to machine code. |
| OpenMPI | 5.0.9-GCC-15.2.0 | The Open MPI Project is an open source MPI-3 implementation. |
| parallel | 20251122-IGB-gcc-15.2.0 | parallel: Build and execute shell commands in parallel |
| pbzip2 | 1.1.13-IGB-gcc-15.2.0 | PBZIP2 is a parallel implementation of the bzip2 block-sorting file compressor that uses pthreads and achieves near-linear speedup on SMP machines. |
| Perl | 5.42.0-GCCcore-15.2.0 | Larry Wall's Practical Extraction and Report LanguageIncludes a small selection of extra CPAN packages for core functionality. |
| Perl-Bundle | 5.42.0-IGB-gcc-15.2.0 | Larry Wall's Practical Extraction and Report Language |
| phobius | 1.01-IGB-gcc-15.2.0 | A combined transmembrane topology and signal peptide predictor |
| phylophlan | 3.2.1-IGB-gcc-15.2.0-Python-3.14.0 | PhyloPhlAn is an integrated pipeline for large-scale phylogenetic profiling of genomes and metagenomes. |
| picard | 3.5.0-Java-25.0.1 | A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format. |
| pigz | 2.8-IGB-gcc-15.2.0 | pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. |
| pybedtools | 0.12.1-IGB-gcc-15.2.0-Python-3.14.0 | pybedtools is a Python package that wraps BEDTools, so you will need both installed. |
| pyBigWig | 0.3.26-IGB-gcc-15.2.0 | A python extension, written in C, for quick access to bigBedfiles and access to and creation of bigWig files. |
| Pysam | 0.24.0-IGB-gcc-15.2.0-Python-3.14.0 | Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. |
| Python | 3.14.0-GCCcore-15.2.0 | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| Python-Bundle | 3.14.0-IGB-gcc-15.2.0 | Python is a programming language that lets you work more quickly and integrate your systems more effectively. |
| PyTorch | 2.14.1-IGB-gcc-15.2.0-Python-3.14.0 | Tensors and Dynamic neural networks in Pythonwith strong GPU acceleration. |
| QIIME2 | 2026.7 | QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. |
| R | 4.6.1-IGB-gcc-15.2.0 | R is a free software environment for statistical computing and graphics. |
| Raven | 1.8.3-IGB-gcc-15.2.0 | Raven is a de novo genome assembler for long uncorrected reads. |
| Rust | 1.92.0-GCCcore-15.2.0 | Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. |
| SAMtools | 1.22-IGB-gcc-15.2.0 | SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. |
| sentieon | 202503 | A fast and accurate solution to variant calling from next-generation sequence data |
| spaceranger | 4.1.0 | Space Ranger is a set of analysis pipelines that process Visium spatial RNA-seq output and brightfield and fluorescence microscope images in order to detect tissue, align reads, generate feature-spot matrices, perform clustering and gene expression analysis, and place spots in spatial context on the slide image. |
| SQLite | 3.50.1-GCCcore-15.2.0 | SQLite: SQL Database Engine in a C Library |
| ssqueezepy | 0.6.6-IGB-gcc-15.2.0-Python-3.14.0 | Synchrosqueezing is a powerful reassignment method that focuses time-frequency representations, and allows extraction of instantaneous amplitudes and frequencies. |
| STAR | 2.7.11b-IGB-gcc-15.2.0 | STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. |
| SUPPA | 2.4-IGB-gcc-15.2.0-Python-3.14.0 | Fast, accurate, and uncertainty-aware differential splicing analysis across multiple conditions. |
| sympy | 1.14.0-IGB-gcc-15.2.0-Python-3.14.0 | SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. |
| TensorFlow | 2.21.0 | An open-source software library for Machine Intelligence |
| Trycycler | 0.5.6-IGB-gcc-15.2.0-Python-3.14.0 | Trycycler is a tool for generating consensus long-read assemblies for bacterial genomes. I.e. if you have multiple long-read assemblies for the same isolate, Trycycler can combine them into a single assembly that is better than any of your inputs. |
| udunits | 2.2.28-GCCcore-15.2.0 | UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. |
| umap-learn | 0.5.12-IGB-gcc-15.2.0-Python-3.14.0 | Uniform Manifold Approximation and Projection (UMAP) is a dimension reduction technique that can be used for visualisation similarly to t-SNE, but also for general non-linear dimension reduction. |
| VCFtools | 0.1.17-IGB-gcc-15.2.0-Perl-5.42.0 | The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. |
| vsearch | 2.30.2-IGB-gcc-15.2.0 | The aim of this project is to create an alternative to the USEARCH tool developed by Robert C. Edgar (2010). The new tool should: |
| Zip | 3.0-GCCcore-15.2.0 | Zip is a compression and file packaging/archive utility.Although highly compatible both with PKWARE's PKZIP and PKUNZIPutilities for MS-DOS and with Info-ZIP's own UnZip, our primary objectiveshave been portability and other-than-MSDOS functionality |