Application updates in the last 3 months
To see all versions available for any application, use module avail application_name
All centrally-installed applications are listed on the Applications page
Updated Application
22 Sep 2023 cellranger updated to version 7.2.0
Cell Ranger is a set of analysis pipelines that processes Chromium single cell 3’ RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis.
22 Sep 2023 dotnet updated to version 6.0.22
.NET Core Runtime
22 Sep 2023 fragpipe updated to version 20.0
FragPipe is a Java Graphical User Interface (GUI) and CLI workflow tool for a suite of computational tools enabling comprehensive analysis of mass spectrometry-based proteomics data. It is powered by MSFragger.
22 Sep 2023 msfragger updated to version 3.8
An ultrafast database search tool for peptide identification in mass spectrometry-based proteomics.
22 Sep 2023 ionquant updated to version 1.9.8
IonQuant is a fast and comprehensive tool for MS1 precursor intensity-based quantification for timsTOF PASEF DDA and non-timsTOF (e.g., Orbitrap) data. It enables label-free quantification with false discovery (FDR) controlled match-between-runs (MBR). It can also be used for quantification in labelling-based experiments such as those involving SILAC, dimethyl, or similar labelling strategies. IonQuant is available as part of FragPipe (recommended option), but can also be run as a command-line tool.
21 Sep 2023 epic2 updated to version 0.0.52
epic2 is an ultraperformant reimplementation of SICER. It focuses on speed, low memory overhead and ease of use.
20 Sep 2023 CTF updated to version 6.1
The CTF MEG software has two main roles: - Provide a human-machine interface to the CTF MEG elec- tronics to collect MEG and/or EEG data. - Provide a tool for reviewing and (to a limited extent) ana- lyzing the MEG and/or EEG data acquired by the CTF MEG system.
18 Sep 2023 xcp_d updated to version 0.5.0
xcp_d is a postprocessing and noise regression pipeline for fMRI datasets (can use output from fmriprep and nibabies).
17 Sep 2023 esm updated to version 2.0.0-74-g2b36991
Code and pre-trained weights for Transformer protein language models from the Meta Fundamental AI Research Protein Team (FAIR)
13 Sep 2023 nextflow updated to version 23.04.3
Data-driven computational pipelines
13 Sep 2023 AlphaPulldown updated to version 0.30.7
AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command-line interface, a variety of confidence scores and a graphical analysis tool.
12 Sep 2023 picard updated to version 3.1.0
Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.
12 Sep 2023 fcs updated to version 0.4.0
FCS is a toolset to remove contaminant sequences from a genome assembly.
12 Sep 2023 medaka updated to version 1.9.1
medaka is a tool to create a consensus sequence from nanopore sequencing data. This task is performed using neural networks applied from a pileup of individual sequencing reads against a draft assembly.
11 Sep 2023 verkko updated to version 1.4.1
Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads.
11 Sep 2023 bonito updated to version 0.7.2
A PyTorch Basecaller for Oxford Nanopore Reads
11 Sep 2023 dxda updated to version 0.6.0
CLI tool to manage the download of large quantities of files from DNAnexus
11 Sep 2023 rust updated to version 1.72.0
A language empowering everyone to build reliable and efficient software.
11 Sep 2023 snakemake updated to version 7.32.3
Snakemake aims to reduce the complexity of creating workflows by providing a fast and comfortable execution environment, together with a clean and modern domain specific specification language (DSL) in python style. It is well suited for bioinformatic workflows.
11 Sep 2023 quarto updated to version 1.3.450
Quarto is an open-source scientific and technical publishing system built on Pandoc
11 Sep 2023 golang updated to version 1.21.1
The Go programming language
11 Sep 2023 gutSMASH updated to version 0-20210610
gutSMASH is a tool that has been developed to systematically evaluate the metabolic potential of anaerobic bacteria in the gut by predicting both known and novel anaerobic metabolic gene clusters from the gut microbiome.
7 Sep 2023 checkm2 updated to version 1.0.2
Rapid assessment of genome bin quality using machine learning.
6 Sep 2023 pdb2pqr updated to version 3.6.1
Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling
6 Sep 2023 dorado updated to version 0.3.4
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
6 Sep 2023 guppy updated to version 6.5.7
Local accelerated basecalling for Nanopore data
6 Sep 2023 parallel updated to version 20230822
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
6 Sep 2023 netOglyc updated to version 4.0
NetOglyc produces neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
31 Aug 2023 sequencetubemap updated to version 2023.8
A JavaScript module for the visualization of genomic sequence graphs. It automatically generates a "tube map"-like visualization of sequence graphs which have been created with vg.
31 Aug 2023 DeepCell-tf updated to version 0.12.6
The DeepCell-tf library allows users to apply pre-existing models to imaging data as well as to develop new deep learning models for single-cell analysis. The library specializes in models for cell segmentation (whole-cell and nuclear) in 2D and 3D images as well as cell tracking in 2D time-lapse datasets. The models are applicable to data ranging from multiplexed images of tissues to dynamic live-cell imaging movies.
31 Aug 2023 ROBOT updated to version 1.9.4
ROBOT is a command-line tool and library for automating ontology development tasks, with a focus on Open Biological and Biomedical Ontologies (OBO). It can be used as a command-line tool or as a library for any language on the Java Virtual Machine.
30 Aug 2023 cytotrace updated to version 0.3.3
CytoTRACE (Cellular (Cyto) Trajectory Reconstruction Analysis using gene Counts and Expression) is a computational method that predicts the differentiation state of cells from single-cell RNA-sequencing data. CytoTRACE leverages a simple, yet robust, determinant of developmental potential—the number of detectably expressed genes per cell, or gene counts. We have validated CytoTRACE on ~150K single-cell transcriptomes spanning 315 cell phenotypes, 52 lineages, 14 tissue types, 9 scRNA-seq platforms, and 5 species.
30 Aug 2023 plastimatch updated to version 1.9.3
Application for registration of medical images such as X-rays, CT, MRI and PET
28 Aug 2023 AFNI updated to version current-py3
AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity.
24 Aug 2023 paraview updated to version 5.11.1
ParaView is an open-source, multi-platform data analysis and visualization application.
24 Aug 2023 CIRCLE-seq updated to version 1.1
CIRCLE-seq is a tool ifor analysis of circularization for in vitro reporting of cleavage effects by sequencing. It is a highly sensitive, sequencing-efficient in vitro screening strategy that outperforms existing cell-based or biochemical approaches for identifying CRIScrisPR–Cas9 genome-wide off-target mutations. It can be practiced using widely accessible next-generation sequencing technology and does not require reference genome sequences. Importantly, CIRCLEcircle-seq can be used to identify off-target mutations associated with cell-type-specific single-nucleotide polymorphisms, demonstrating the feasibility and importance of generating personalized specificity profiles.
22 Aug 2023 Matlab updated to version 2023a
MATLAB is an interactive software package for scientific and engineering numeric computation. MATLAB integrates numerical analysis, matrix computation, signal processing, and graphics in an environment where problems and solutions are expressed just as they are written mathematically.
18 Aug 2023 napari updated to version 0.4.18
napari is an image viewer.Can be used to annotate images.
16 Aug 2023 focus updated to version 0.802
FOCUS (Fine-mapping Of CaUsal gene Sets) is software to fine-map transcriptome-wide association study statistics at genomic risk regions. The software takes as input summary GWAS data along with eQTL weights and outputs a credible set of genes to explain observed genomic risk.
15 Aug 2023 fmriprep updated to version 23.1.4
A Robust Preprocessing Pipeline for fMRI Data
15 Aug 2023 mriqc updated to version 23.1.0
MRIQC is an MRI quality control tool
11 Aug 2023 shasta updated to version 0.11.1
De novo assembly from Oxford Nanopore reads
10 Aug 2023 Mathematica updated to version 13.3.0
Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language.
8 Aug 2023 tomotwin updated to version 0.5.0
TomoTwin - a deep metric learning based particle picking procedure for cryo-ET
3 Aug 2023 megit updated to version 0.4.0
Minimal Eclipe GIT. A graphical front end for git based off the eclipse IDE.
3 Aug 2023 flanker updated to version 0.1.5
Gene-flank analysis tool
2 Aug 2023 fithic updated to version 2.0.8
Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.
1 Aug 2023 Perl updated to version 5.38
Perl is a highly capable, feature-rich programming language with over 30 years of development.
1 Aug 2023 htseq updated to version 2.0.4
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
1 Aug 2023 nested updated to version 2.0.0
nested (now also called TE-greedy) is software to analyze nested LTR transposable elements in DNA sequences, such as reference genomes.
28 Jul 2023 pvactools updated to version 4.0.1
pVACtools is a cancer immunotherapy suite consisting of pVACseq, pVACfuse, pVACvector
28 Jul 2023 PartekFlow updated to version
Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.
28 Jul 2023 Genome Browser updated to version 451
The Genome Browser Mirror Fragments is a mirror of the UCSC Genome Browser. The URL is Users can also access the MySQL databases, supporting files directly, and a huge number of associated executables.
27 Jul 2023 chap updated to version 0.9.1
CHAP is a tool for the functional annotation of ion channel structures
27 Jul 2023 model-angelo updated to version 1.0.1
ModelAngelo is an automatic atomic model building program for cryo-EM maps.
27 Jul 2023 fastq_demux updated to version 20230713
fastq_demux is a simple program to demultiplex a FASTQ file or a pair of FASTQ files based on the barcodes present in the FASTQ headers.
27 Jul 2023 libfreetype updated to version 2.13.1
FreeType is a freely available software library to render fonts.
27 Jul 2023 Rosetta updated to version 2023.26
The Rosetta++ software suite can perform de novo protein structure predictions, identify low free energy sequences for target protein backbones, predict the structure of a protein-protein complex from the individual structures of the monomer components, incorporate NMR data into the basic Rosetta protocol to accelerate the process of NMR structure prediction, and more...
26 Jul 2023 fusioninspector updated to version 2.6.0
In silico Validation of Fusion Transcript Predictions
26 Jul 2023 mosaics updated to version 1.0.0
A collection of tools for characterizing membrane structure and dynamics within simulated trajectories of molecular systems.
26 Jul 2023 xtail updated to version 1.1.5
Xtail is an analysis pipeline tailored for ribosome profiling data that comprehensively and accurately identifies differentially translated genes in pairwise comparisons. Applied on simulated and real datasets, Xtail exhibits high sensitivity with minimal false-positive rates, outperforming existing methods in the accuracy of quantifying differential translations.
26 Jul 2023 rdfind updated to version 1.6.0
rdfind is a program that finds duplicate files. It is useful for compressing backup directories or just finding duplicate files. It compares files based on their content, NOT on their file names. After typing module load rdfind, type man rdfind for more information.
26 Jul 2023 MySQL updated to version 8.0.34
MySQL is an open-source relational database management system.
26 Jul 2023 graphmap updated to version 0.5.2
GraphMap is a highly sensitive and accurate mapper for long, error-prone reads. It offers a number of valuable features, such as mapping position agnostic to alignment parameters, high sensitivity and precision, handling circular genomes, meaningful mapping quality, various alignment strategies, and more.
26 Jul 2023 boost updated to version 1.82
Boost provides free peer-reviewed portable C++ source libraries. Boost libraries are intended to be widely useful, and usable across a broad spectrum of applications.
26 Jul 2023 picrust updated to version 2.5.2
PICRUSt is a bioinformatics software package designed to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes.
26 Jul 2023 deepmedic updated to version 0.8.4
This project aims to offer easy access to Deep Learning for segmentation of structures of interest in biomedical 3D scans. It is a system that allows the easy creation of a 3D Convolutional Neural Network, which can be trained to detect and segment structures if corresponding ground truth labels are provided for training. The system processes NIFTI images, making its use straightforward for many biomedical tasks.
26 Jul 2023 CCP4 updated to version 8.0.013
CCP4 is a suite of programs for protein crystallography and structural biology.
25 Jul 2023 MINTIE updated to version 0.4.2
MINTIE is a tool for identifying novel, rare transcriptional variants in cancer RNA-seq data. MINTIE detects gene fusions, transcribed structural variants, novel splice variants and complex variants, and annotates all novel transcriptional variants.
25 Jul 2023 EMAN2 updated to version 2.99
EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes.
25 Jul 2023 zstd updated to version 1.5.5
Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios.
25 Jul 2023 inkscape updated to version 1.3
Inkscape is a Free and open source vector graphics editor
25 Jul 2023 azure_cli updated to version 2.50.0
25 Jul 2023 talon updated to version 5.0-60-g2e538a8
TALON is a Python package for identifying and quantifying known and novel genes/isoforms in long-read transcriptome data sets.
24 Jul 2023 pb-cpg-tools updated to version 2.3.1
Tools for analyzing CpG/5mC data from PacBio HiFi reads aligned to a reference genome
23 Jul 2023 vcfpy updated to version 0.13.6
Python library for handling the variant call format. Differs from pyvcf in that it has the ability to modify per-sample genotype information.
23 Jul 2023 nodejs updated to version 18.17.0
Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs
23 Jul 2023 rmblast updated to version 2.14.0
RMBlast is a RepeatMasker-compatible version of the standard NCBI blastn program. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program.
23 Jul 2023 k8 updated to version 0.2.5
javascript shell based on v8, but with fasta/fastq parser and the ability to open files on the filesystem
21 Jul 2023 VEP updated to version 110
VEP (Variant Effect Predictor) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions.
20 Jul 2023 visidata updated to version 2.11.1
VisiData is an interactive multitool for tabular data
19 Jul 2023 DNAnexus updated to version 0.352.1
DNAnexus is a cloud-based commercial solution for next-generation sequence analysis and visualization. It has a command-line interface (CLI) which can be used to log in to the DNAnexus platform, upload and navigate data, and launch analyses.
13 Jul 2023 interproscan updated to version 5.63-95.0
InterProScan is the software package that allows sequences (protein and nucleic) to be scanned against InterPro's signatures. Signatures are predictive models, provided by several different databases, that make up the InterPro consortium.
13 Jul 2023 modkit updated to version 0.1.11
A bioinformatics tool for working with modified bases from Oxford Nanopore. Specifically for converting modBAM to bedMethyl files using best practices, but also manipulating modBAM files and generating summary statistics.
12 Jul 2023 spaceranger updated to version 2.1.0
10x pipeline for processing Visium spatial RNA-seq data
12 Jul 2023 braker updated to version 3
A pipeline for fully automated prediction of protein coding gene structures with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes.
12 Jul 2023 3DSlicer updated to version 5.2.2
A software platform for the analysis (including registration and interactive segmentation) and visualization (including volume rendering) of medical images and for research in image guided therapy.
11 Jul 2023 novocraft updated to version 4.03.08
Package includes aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.
10 Jul 2023 cactus updated to version 2.6.4
Cactus is a reference-free whole-genome multiple alignment program.
10 Jul 2023 RepeatMasker updated to version 4.1.5
RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program.
9 Jul 2023 Julia updated to version 1.9.2
high level, dynamic language for technical computing
7 Jul 2023 CompuCell3D updated to version 4.4.0
CompuCell3D is a multiscale multicellular virtual tissue modeling and simulation environment. CompuCell3D is written in C++ and provides Python bindings for model and simulation development in Python. CompuCell3D is supported on Windows, Mac and Linux.
7 Jul 2023 crypt4gh updated to version 0.4.1
Rust implementation for the Crypt4GH encryption format.
7 Jul 2023 cogentap updated to version 2.0.1
Cogent NGS Analysis Pipeline (CogentAP) is bioinformatic software for analyzing RNA-seq NGS data generated using various takara kits.
6 Jul 2023 cgpbigwig updated to version 1.6.0
BigWig manpulation tools using libBigWig and htslib
6 Jul 2023 gtdb-tk updated to version 2.3.2
GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy
5 Jul 2023 toga updated to version 1.1.2
TOGA is a new method that integrates gene annotation, inferring orthologs and classifying genes as intact or lost. TOGA implements a novel machine learning based paradigm to infer orthologous genes between related species and to accurately distinguish orthologs from paralogs or processed pseudogenes. This tutorial explains how to get started using TOGA. It shows how to install and execute TOGA, and how to handle possible issues that may occur.
5 Jul 2023 Freesurfer updated to version 7.4.1
Freesurfer is a set of automated tools for reconstruction of the brain's cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface.
2 Jul 2023 slivar updated to version 0.3.0
slivar is a set of command-line tools that enables rapid querying and filtering of VCF files. It facilitates operations on trios and groups and allows arbitrary expressions using simple javascript.
30 Jun 2023 tandem-genotypes updated to version 1.9.0
tandem-genotypes finds changes in length of tandem repeats, from "long" DNA reads aligned to a genome.
30 Jun 2023 Schrodinger updated to version 2023.1
A limited number of Schrödinger applications are available on the Biowulf cluster through the Molecular Modeling Interest Group. Most are available through the Maestro GUI.
29 Jun 2023 eigensoft updated to version 8.0.0
The EIGENSOFT package combines functionality from population genetics methods and EIGENSTRAT stratification correction method.
28 Jun 2023 OpenSlide updated to version 3.4.1
OpenSlide is a C library for reading and manipulating digital slides of diverse vendor formats. It provides a simple interface to read whole-slide images (also known as virtual slides). OpenSlide has been used in the digital pathology projects.
28 Jun 2023 globus-cli updated to version 3.15.0
Globus command line interface
27 Jun 2023 mbg updated to version 1.0.15
Minimizer based sparse de Bruijn Graph constructor.
27 Jun 2023 dynamo updated to version 1.1.532
Dynamo is a software environment for subtomogram averaging of cryo-EM data.
26 Jun 2023 pyega3 updated to version 5.0.2
A download client for the European Genome-phenome Archive (EGA). The EGA is designed to be a repository for all types of sequence and genotype experiments, including case-control, population, and family studies.
26 Jun 2023 niftilib updated to version 3.0.0
Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. nifti-1 is a binary file format for storing medical image data, e.g. magnetic resonance image (MRI) and functional MRI (fMRI) brain images.
Scientific Databases updated in last 3 months
For a full list of scientific databases available on the NIH HPC systems, see this page

Updated Database Format Location
20 Sep 2023Protein Data BankBlast/fdb/blastdb/pdbaa
20 Sep 2023SwissProtBlast/fdb/blastdb/swissprot
20 Sep 2023NCBI ntBlast/fdb/blastdb/nt
16 Sep 2023NCBI nrBlast/fdb/blastdb/nr
11 Sep 2023Protein Data BankBlast/fdb/blastdb/pdbnt
01 Aug 2023NCBI ntFasta/fdb/fastadb/nt.fas
01 Aug 2023NCBI nrFasta/fdb/fastadb/nr.fas
01 Aug 2023SwissProtFasta/fdb/fastadb/swissprot.aa.fas
01 Aug 2023Protein Data BankFasta/fdb/fastadb/pdb.aa.fas
26 Jun 2023Mouse Genome (Mus musculus) mm8MySQLNIH mirror of UCSC Genome Browser