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
13 Jun 2024 cnvkit updated to version 0.9.11
Copy number variant detection from targeted DNA sequencing
13 Jun 2024 csvkit updated to version 2.0.0
csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.
13 Jun 2024 deeptools updated to version 3.5.5
deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing DNA sequencing experiments.
13 Jun 2024 hwatch updated to version 0.3.10
A modern alternative to the watch command, records the differences in execution results and can check these differences later.
13 Jun 2024 cactus updated to version 2.8.2
Cactus is a reference-free whole-genome multiple alignment program.
12 Jun 2024 Rstudio updated to version 2024.04.2-764
RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.
11 Jun 2024 vcf2maf updated to version 1.6.22
A smarter, more reproducible, and more configurable tool for converting a VCF to a MAF.
11 Jun 2024 gnuplot updated to version 6.0.1
Gnuplot is a portable command-line driven graphing utility to visualize mathematical functions and data interactively, and can support many non-interactive uses such as web scripting.
Type 'gnuplot' to run, or 'module avail gnuplot' to see other available versions.
11 Jun 2024 mpich updated to version 4.2.1
MPICH is a high-performance and widely portable implementation of the Message Passing Interface (MPI) standard (both MPI-1 and MPI-2).
10 Jun 2024 htseq updated to version 2.0.7
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
10 Jun 2024 fanc updated to version 0.9.28
FAN-C is a toolkit for the analysis and visualization of Hi-C data. Beyond objects generated within FAN-C, the toolkit is largely compatible with Hi-C files from Cooler and Juicer.
10 Jun 2024 Genome Browser updated to version 465
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.
10 Jun 2024 apptainer updated to version 1.3.2
Apptainer allows you to build and run Linux containers with emphasis on use in HPC. Apptainer is the Linux Foundation variant of and successor to the widely popular Singularity.
9 Jun 2024 PartekFlow updated to version
Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.
9 Jun 2024 LAST updated to version 1544
LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:
  • Finding rearrangements and recombinations (last-split)
  • Finding DNA-versus-protein related regions, especially protein fossils.
  • Unusual data, e.g. AT-rich DNA, because it can fit parameters to the data and calculate significance.
  • Sensitive DNA-DNA search, due to fitting, sensitive seeding, and calculating significance.
9 Jun 2024 vcfpy updated to version 0.13.8
Python library for handling the variant call format. Differs from pyvcf in that it has the ability to modify per-sample genotype information.
9 Jun 2024 htsbox updated to version r350
HTSbox is a fork of early HTSlib. It is a collection of small experimental tools manipulating HTS-related files. While some of these tools are already part of the official SAMtools package, others are for niche use cases.
9 Jun 2024 k8 updated to version 1.2
javascript shell based on v8, but with fasta/fastq parser and the ability to open files on the filesystem
7 Jun 2024 slivar updated to version 0.3.1
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.
6 Jun 2024 rapids-singlecell updated to version 0.10.4
Rapids-singlecell offers enhanced single-cell data analysis as a near drop-in replacement predominantly for scanpy.Utilizing GPU computing with cupy and Nvidia’s RAPIDS, it emphasizes high computational efficiency.
5 Jun 2024 FFmpeg updated to version 7.0.1
A complete, cross-platform solution to record, convert and stream audio and video.
4 Jun 2024 stringtie updated to version 2.2.3
StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de novo genome assembly to help with transcript assembly.
4 Jun 2024 dorado updated to version 0.7.1
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
4 Jun 2024 novocraft updated to version 4.04.01
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.
3 Jun 2024 inkscape updated to version 1.3.2
Inkscape is a Free and open source vector graphics editor
3 Jun 2024 subread updated to version 2.0.6
High-performance read alignment, quantification and mutation discovery
1 Jun 2024 medaka updated to version 1.12.0
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.
31 May 2024 verkko updated to version 2.1
Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads.
31 May 2024 ngsrelate updated to version 2.0
NgsRelate can be used to infer relatedness, inbreeding coefficients and many other summary statistics for pairs of individuals from low coverage Next Generation Sequencing (NGS) data by using genotype likelihoods instead of called genotypes.
30 May 2024 boost updated to version 1.85
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.
29 May 2024 toga updated to version 1.1.7
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.
29 May 2024 Huygens updated to version 24.04
Huygens is an image restoration, deconvolution, resolution and noise reduction. It can process images from all current optical microscopes, including wide-field, confocal, Nipkow (scanning disk confocal), multiple-photon, and 4Pi microscopes.
29 May 2024 parallel updated to version 20240522
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
29 May 2024 strainge updated to version 1.3.9
StrainGE is a set of tools to analyse the within-species strain diversity in bacterial populations. It consists of two main components: 1) StrainGST: Strain Genome Search tool, a tool to find close reference genomes for strains present in a sample and 2) StrainGR: Strain Genome Recovery, a tool to perform strain-aware variant calling at low coverages.
29 May 2024 nextflow updated to version 24.04.1
Data-driven computational pipelines
28 May 2024 sratoolkit updated to version 3.1.1
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
27 May 2024 pggb updated to version 0.6.0
pangenome graph builder.
23 May 2024 modkit updated to version 0.3.0
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.
21 May 2024 obc2fastq updated to version 6.0.0
The PacBio obc2fastq software is designed for use with Onso sequencing data. You can demultiplex samples and generate FASTQ files for use with downstream data pipelines through a command-line interface.
21 May 2024 rstudio-server updated to version 2024.04.1-748
RStudio Server is a web-based R IDE similar to RStudio Desktop.
20 May 2024 cellranger updated to version 8.0.1
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.
20 May 2024 immcantation updated to version 4.5.0
The Immcantation framework provide a start-to-finish analytical ecosystem for high-throughput AIRR-seq datasets. Immcantation includes Alakazam, Change-O, Dowser, pRESTO, SCOPer, SHazaM, and TIgGER.
15 May 2024 cromwell updated to version 87
A Workflow Management System geared towards scientific workflows.
15 May 2024 rust updated to version 1.78.0
A language empowering everyone to build reliable and efficient software.
15 May 2024 jellyfish updated to version 2.3.1
Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA.
15 May 2024 IGV updated to version 2.17.4
The Integrative Genomics Viewer is a high-performance visualization tool for interactive exploration of large, integrated genomic datasets.
12 May 2024 sniffles updated to version 2.3.3
Sniffles is a structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis.
12 May 2024 nvchecker updated to version 2.14.1
nvchecker (short for new version checker) is for checking if a new version of some software has been released.
10 May 2024 chopper updated to version 0.8.0
Filtering and trimming for long-read sequencing data (PacBio/ONT).
10 May 2024 hifiasm updated to version 0.19.9
Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. Its latest release supports telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads. It can produce better haplotype-resolved assemblies when given parental short reads or Hi-C data.
10 May 2024 tedana updated to version 24.0.1
Tedana is an application to denoise multi-echo fMRI datasets
10 May 2024 fzf updated to version 0.52.0
A command-line fuzzy finder
10 May 2024 eza updated to version 0.18.15
A modern, maintained replacement for ls. A replacement for the now-unmaintained exa.
9 May 2024 dust updated to version 1.0.0
Like du but more intuitive. dust provides an easy-to-use visualization tool for disk space usage allow you to easily find the subfolders eating up all of your quota.
9 May 2024 extrautils updated to version 1.0
Extra command line utilities not available by default, all in one convenient location, as simple as module load extrautils.
9 May 2024 ncdu updated to version 1.20
ncdu is an interactive disk usage analyzer with a text UI designed to find space-hogging directories.
9 May 2024 fd updated to version 10.1.0
fd is a simple, fast and user-friendly alternative to find. While it does not aim to support all of find's powerful functionality, it provides sensible (opinionated) defaults for a majority of use cases.
8 May 2024 splam updated to version 1.0.10
Splice junction recognition model based on a deep residual convolutional neural network to assess splice junctions.
8 May 2024 miniwdl updated to version 1.12.0
A Workflow Description Language local runner. An alternative to Cromwell for running WDL pipelines
7 May 2024 metaminimac2 updated to version 973bd27
tool to combine genotype data imputed against multiple reference panels.
7 May 2024 metaphlan updated to version 4.1.0
MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling.
7 May 2024 humann updated to version 3.9.0
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
6 May 2024 trgt updated to version 1.0.0
TRGT is a tool for targeted genotyping of tandem repeats from PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat. TRGT comes with a companion tool TRVZ for visualization of reads overlapping the repeats.
3 May 2024 R updated to version 4.4.0
R (the R Project) is a language and environment for statistical computing and graphics. R is similar to S, and provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...).
3 May 2024 SciTE updated to version 5.5.0
SciTE or SCIntilla based Text Editor is a cross-platform text editor. Lightweight and built for speed, it is designed mainly for source editing, and performs syntax highlighting and inline function reference for many different languages.
29 Apr 2024 VADR updated to version 1.5.1
VADR stands for Viral Annotation DefineR. It is a suite of tools for classifying and analyzing sequences homologous to a set of reference models of viral genomes or gene families. It has been mainly tested for analysis of Norovirus, Dengue, and SARS-CoV-2 virus sequences in preparation for submission to the GenBank database.
29 Apr 2024 libvips updated to version 8.15.1
libvips is a demand-driven, horizontally threaded image processing library. Compared to similar libraries, libvips runs quickly and uses little memory.
26 Apr 2024 xeniumranger updated to version
Pipeline to process Xenium In Situ Gene Expression data
26 Apr 2024 rtg-tools updated to version 3.8.4
variant detection for singletons, families, large pedigrees and populations, cancer, structural variant and CNV analysis, and microbial and metagenomic analysis
26 Apr 2024 pod5 updated to version 0.3.10
Tool for manipulating the pod5 format of nanopore reads
22 Apr 2024 fcs updated to version 0.5.0
FCS is a toolset to remove contaminant sequences from a genome assembly.
17 Apr 2024 NAMD updated to version 3.0beta6
NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. VMD, the associated molecular visualization program, is also available.
17 Apr 2024 GeoMX NGS Pipeline updated to version
The GeoMx NGS Pipeline, processes RNA-sequencing files (FASTQ files) from Illumina sequencers according to parameters defined in the Configuration File (which is generated from the GeoMx DSP run). The Pipeline processes information from these files and outputs .dcc files, which can then be uploaded to the GeoMx DSP system for data analysis.
16 Apr 2024 manorm updated to version 1.3.0
MAnorm is for quantitative comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifications. The quantitative binding differences inferred by MAnorm showed strong correlation with both the changes in expression of target genes and the binding of cell type-specific regulators.
14 Apr 2024 nodejs updated to version 20.12.2
Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs
14 Apr 2024 smrtanalysis updated to version 13.1
SMRT® Analysis is a bioinformatics software suite available for analysis of DNA sequencing data from Pacific Biosciences’ SMRT technology. Users can choose from a variety of analysis protocols that utilize PacBio® and third-party tools. Analysis protocols include de novo genome assembly, cDNA mapping, DNA base-modification detection, and long-amplicon analysis to determine phased consensus sequences.
8 Apr 2024 motioncor3 updated to version 1.0.1
An improved implementation of MotionCor2 with addition of CTF estimation, Multi-GPU accelerated software package that enables single-pixel level correction of anisotropic beam induced sample motion for cryoEM and cryET images.
5 Apr 2024 pangenome updated to version 1.1.2
nf-core/pangenome is a bioinformatics best-practise analysis pipeline for the rendering of a collection of sequences into a pangenome graph.
5 Apr 2024 IDL/ENVI updated to version 9.0/6.0
IDL and ENVI are a complete computing environment for the interactive analysis and visualization of data. IDL integrates an array-oriented language with mathematical analysis and graphical display techniques. ENVI is designed for extracting information from geospatial and medical imagery.
2 Apr 2024 tomotwin updated to version 0.8.0
TomoTwin - a deep metric learning based particle picking procedure for cryo-ET
2 Apr 2024 hitips updated to version 1.0.4
HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression. Documentations:
1 Apr 2024 parabricks updated to version 4.3.0
The Clara Parabricks toolkit is a set of GPU-accelerated genome analysis tools for secondary analysis of next generation sequencing data.
29 Mar 2024 genomad updated to version 1.7.6
geNomad's primary goal is to identify viruses and plasmids in sequencing data (isolates, metagenomes, and metatranscriptomes).
29 Mar 2024 minimap2 updated to version 2.28
Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR).
28 Mar 2024 spaceranger updated to version 3.0.0
10x pipeline for processing Visium spatial RNA-seq data
28 Mar 2024 NeST-VNN updated to version 20240321
NeST-VNN is an interpretable neural network-based model that predicts cell response to a drug. This framework integrates information across multiple levels of cancer cell biology to understand drug response, and can serve to identify and explain biomarkers for clinical application.
28 Mar 2024 zstd updated to version 1.5.6
Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios.
27 Mar 2024 stripy-pipeline updated to version 1.2
STRipy-pipeline is non-graphical command-line version of STRipy that can be integrated into pipelines and analyse multiple STR or VNTR loci in parallel.
27 Mar 2024 HBD / heme_binder_diffusion updated to version 20240319
RoseTTAFold All-Atom (RFAA), a deep network capable of modeling full biological assemblies containing proteins, nucleic acids, small molecules, metals, and covalent modifications given the sequences of the polymers and the atomic bonded geometry of the small molecules and covalent modifications. The heme_binder_diffusion pipeline employs RoseTTAFold All-Atom to perform de novo heme binding protein design.
27 Mar 2024 spipe updated to version 1.20.0
Split-pool combinatorial barcoding makes it possible to scale projects to hundreds of samples and millions of cells, overcoming limitations of previous droplet based technologies. Spipe (split-pipe) implements combinatorial barcoding method for single cell RNA sequencing (scRNA-seq) with dramatically improved sensitivity.
26 Mar 2024 cryoDRGN updated to version 1.1.0
CryoDRGN is an algorithm that leverages the representation power of deep neural networks to directly reconstruct continuous distributions of 3D density maps and map per-particle heterogeneity of single-particle cryo-EM datasets. It contains interactive tools to visualize a dataset’s distribution of per-particle variability, generate density maps for exploratory analysis, extract particle subsets for use with other tools and generate trajectories to visualize molecular motions.
26 Mar 2024 rapidtide updated to version 2.8.2
Rapidtide is a suite of Python programs used to model, characterize, visualize, and remove time varying, physiological blood signals from fMRI and fNIRS datasets. The primary workhorses of the package are the rapidtide program, which characterizes bulk blood flow, and happy, which focusses on the cardiac band.
22 Mar 2024 DeepLabCut updated to version 2.3.9
DeepLabCut is an open source toolbox that builds on a state-of-the-art human pose estimation algorithm. It allows training of a deep neural network by using limited training data to precisely track user-defined features, so that the human labeling accuracy will be matched.
22 Mar 2024 gromacs updated to version 2024.1
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. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers.
21 Mar 2024 deepvariant updated to version 1.6.1
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
20 Mar 2024 bowtie2 updated to version 2.5.3
A version of bowtie that's 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
20 Mar 2024 cutadapt updated to version 4.7
cutadapt removes adapter sequences from DNA high-throughput sequencing data. This is usually necessary when the read length of the machine is longer than the molecule that is sequenced, such as in microRNA data.
20 Mar 2024 Tex updated to version 2024
Tex + Latex + associated packages for high-quality text formatting.
19 Mar 2024 Beagle updated to version 5.4_01Mar24
Beagle is a package for imputing genotypes, inferring haplotype phase, and performing genetic association analysis. BEAGLE is designed to analyze large-scale data sets with hundreds of thousands of markers genotyped on thousands of samples.
18 Mar 2024 model-angelo updated to version 1.0.12
ModelAngelo is an automatic atomic model building program for cryo-EM maps.
Scientific Databases updated in last 3 months

For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data