Application updates in the last 3 months
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Updated Application
4 Feb 2025 nodejs updated to version 22.13.1
Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs
4 Feb 2025 trgt updated to version 1.5.0
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 can also create a visualization of reads overlapping the repeats.
4 Feb 2025 hifiasm updated to version 0.24.0
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.
4 Feb 2025 whatshap updated to version 2.4
WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads.
4 Feb 2025 longshot updated to version 1.0.0
Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs).
3 Feb 2025 bwulf updated to version 0.3
unified interface to custom utilities by the NIH HPC staff.
31 Jan 2025 modkit updated to version 0.4.3
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.
29 Jan 2025 Mathematica updated to version 14.2.0
Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language.
29 Jan 2025 ccpem updated to version 1.6.0
The Collaborative Computational Project for electron cryo-microscopy (CCP-EM) supports users and developers in biological cryogenic EM.
27 Jan 2025 famdb updated to version 1.0.5
FamDB is a modular HDF5-based export format and query tool developed for offline access to the Dfam database of transposable element and repetitive DNA families.
27 Jan 2025 PyRosetta updated to version 387.py3.12
PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
27 Jan 2025 pixi updated to version 0.40.3
pixi is a cross-platform, multi-language package manager and workflow tool built on the foundation of the conda ecosystem. It provides developers with an exceptional experience similar to popular package managers like cargo or yarn, but for any language.
23 Jan 2025 OmicCircosShiny updated to version 250121
Shiny wrapper for R OmicCircos package. Only used in OpenOndemand
22 Jan 2025 dorado updated to version 0.9.1
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
22 Jan 2025 Genome Browser updated to version 476
The Genome Browser Mirror Fragments is a mirror of the UCSC Genome Browser. The URL is https://hpcnihapps.cit.nih.gov/genome. Users can also access the MySQL databases, supporting files directly, and a huge number of associated executables.
22 Jan 2025 parallel updated to version 20250122
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
20 Jan 2025 kanpig updated to version 1.0.2
A fast tool for genotyping structural variants with long-reads
17 Jan 2025 xeniumranger updated to version 3.1.0
Pipeline to process Xenium In Situ Gene Expression data
16 Jan 2025 Huygens updated to version 24.10
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.
15 Jan 2025 cryoDRGN updated to version 3.4.3
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.
13 Jan 2025 verkko updated to version 2.2.1
Verkko is a hybrid genome assembly pipeline developed for telomere-to-telomere assembly of PacBio HiFi and Oxford Nanopore reads.
10 Jan 2025 parsnp updated to version 2.1.2
Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees
9 Jan 2025 boltz updated to version 0.4.0
Boltz-1 is the state-of-the-art open-source model to predict biomolecular structures containing combinations of proteins, RNA, DNA, and other molecules. It also supports modified residues, covalent ligands and glycans, as well as conditioning the prediction on specified interaction pockets or contacts.
7 Jan 2025 bwa-meth updated to version 0.2.7
bwa-meth is a tool to align bisulfitetreated sequences and compare it to existing aligners. It is it is fast and accurate even without quality-trimming and the output is immediately usable by downstream tools.
6 Jan 2025 deepdewedge updated to version 241209
DeepDeWedge is A Deep Learning Method for Simultaneous Denoising and Missing Wedge Reconstruction in Cryogenic Electron Tomography".
30 Dec 2024 nextflow updated to version 24.10.3
Data-driven computational pipelines
26 Dec 2024 gapstop updated to version 0.3
GPU-Accelerated Python gapSTOP for Template Matching is an open-source SW for fast template matching (TM) in cryo electron tomograms that is based on TM routines from STOPGAP.
26 Dec 2024 locscale updated to version 2.2.9a
LocScale is a reference-based local amplitude scaling tool using prior model information to improve contrast of cryo-EM density maps. It can be helpful in the common case of resolution variation in the 3D reconstruction and it can be used as an alternative to other commonly applied map sharpening methods.
26 Dec 2024 Open OnDemand updated to version 3.1.10
The Open OnDemand interface allows you to work on the Biowulf cluster via your web browser. You can utilize select interactive web applications like Jupyter, RStudio or VS Code directly without logging in via traditional SSH. You can also access graphical applications via a familiar interface running on compute nodes.
26 Dec 2024 texinfo updated to version 7.2
Texinfo is the official documentation format of the GNU project
26 Dec 2024 gnuplot updated to version 6.0.2
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.
23 Dec 2024 recovar updated to version 20241210
RECOVAR is a software tool for analyzing different conformations in heterogeneous cryo-EM and cryo-ET datasets. RECOVAR can reconstruct high-resolution volumes, estimate conformational density and low free-energy motions, and automatically identify subsets of images with a particular volume feature.
23 Dec 2024 lipidens updated to version 1.0.0
LipIDens is a pipeline for simulation assisted interpretation of lipid or lipid-like densities in e.g. cryogenic electron microscopy (cryo-EM) structures of membrane proteins. The protocol can be used to establish CG simulations, analyse lipid binding sites using PyLipID, screen, rank and process PyLipID outputs and establish atomistic simulations to refine lipid binding poses.
20 Dec 2024 interproscan updated to version 5.72-103.0
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.
20 Dec 2024 transcript_clean updated to version 2.1
TranscriptClean is a Python program that corrects mismatches, microindels, and noncanonical splice junctions in long reads that have been mapped to the genome. It is designed for use with sam files from the PacBio Iso-seq and Oxford Nanopore transcriptome sequencing technologies
19 Dec 2024 SciTE updated to version 5.5.4
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.
19 Dec 2024 ChimeraX updated to version 1.9
UCSF ChimeraX (or simply ChimeraX) is the next-generation molecular visualization program from the Resource for Biocomputing, Visualization, and Informatics (RBVI), following UCSF Chimera.
19 Dec 2024 saturn updated to version 6906abf
Saturn is a deep learning approach that couples gene expression with protein representations learnt using large protein language models for cross-species integration. The key idea in SATURN is to map cells from all datasets to a shared space of functionally related genes that we name macrogenes. Using macrogenes, SATURN is uniquely able to detect functionally related genes co-expressed across species.
18 Dec 2024 IMOD updated to version 5.1.0
IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections.
18 Dec 2024 QIIME updated to version 2024.10
QIIME is an open source software package for comparison and analysis of microbial communities, primarily based on high-throughput amplicon sequencing data (such as SSU rRNA) generated on a variety of platforms, but also supporting analysis of other types of data (such as shotgun metagenomic data).
18 Dec 2024 cutadapt updated to version 5.0
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.
18 Dec 2024 aretomo3 updated to version 2.0.3
AreTomo3 is a multi-GPU accelerated software package that enables real-time fully automated reconstruction of cryoET tomograms in parallel with cryoET data collection. Integrating MotionCor3, AreTomo2, and GCtfFind in a single application, AreTomo3 has established an autonomous preprocessing pipeline that, whenever a new tilt series is collected, can activate and repeat itself from correction of beam induced motion and assembling tilt series to CTF estimation and correction, tomographic alignment, and 3D reconstruction throughout entire session of data collection without human intervention.
17 Dec 2024 LAST updated to version 1607
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.
17 Dec 2024 sniffles updated to version 2.5.3
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.
17 Dec 2024 warp updated to version 2.0.0dev31
Warp is a set of tools for cryo-EM and cryo-ET data processing including: Warp, M, WarpTools, MTools, MCore, and Noise2Map.
16 Dec 2024 smrtanalysis updated to version 25.1
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.
16 Dec 2024 genotools updated to version 1.3.2
GenoTools is a suite of automated genotype data processing steps written in Python. The core pipeline was built for Quality Control and Ancestry estimation of data in the Global Parkinson's Genetics Program (GP2).
16 Dec 2024 AreTomo2 updated to version 1.1.2
A multi-GPU accelerated software package that fully automates motion-corrected marker-free tomographic alignment and reconstruction. It is improved version of AreTomo that allow multi-gpu parallelization and better tilt-series alignment.
16 Dec 2024 HLA-LA updated to version 1.0.4
Fast HLA type inference from whole-genome data. Previously known as HLA-PRG-LA.
16 Dec 2024 cellbender updated to version 0.3.2
CellBender is a software package for eliminating technical artifacts from high-throughput single-cell omics data, including scRNA-seq, snRNA-seq, and CITE-seq.
15 Dec 2024 PartekFlow updated to version 12.3.0
Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.
13 Dec 2024 blender updated to version 4.3
Blender is the free and open source 3D creation suite. Blender on Biowulf is meant for command-line rendering.
12 Dec 2024 BEAST updated to version 10.5.0,2.6.7
BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences.
12 Dec 2024 foldseek updated to version 9-427df8a
Fast structural similarity search
12 Dec 2024 cdnacupcake updated to version 29.0.0
Miscellaneous collection of Python and R scripts for processing Iso-Seq data
11 Dec 2024 portal_client updated to version 1.4.5
Portal_client is Python-based client for downloading data made available through portals powered by the GDC-based portal system. There are several portals running on the internet to support various research efforts. Notably, the Neuroscience Multi-omic Archive (NeMO, https://nemoarchive.org/) and the Human Microbiome Project Data Analysis and Coordination Center (hmpdacc.org) use the portal to enable data exploration and download. The client accepts a manifest file as an input. This file contains URLs to the files to be downloaded. Manifest files can be generated using the shopping cart functionality of the portal's query interface.
11 Dec 2024 bakta updated to version 1.10.2
Rapid & standardized annotation of bacterial genomes, MAGs & plasmids
9 Dec 2024 deepvariant updated to version 1.8.0
DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.
4 Dec 2024 Qt updated to version 5.15.16
Qt is a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed.
4 Dec 2024 xpdf updated to version 4.05
Xpdf is a free PDF viewer and toolkit, including a text extractor, image converter, HTML converter, and more. Most of the tools are available as open source.
4 Dec 2024 alphafold3 updated to version 3.0.0
This package provides an implementation of the inference pipeline of AlphaFold 3
4 Dec 2024 virtualgl updated to version 3.1.1
VirtualGL is an open source toolkit that gives any Unix or Linux remote display software the ability to run OpenGL applications with full 3D hardware acceleration.
2 Dec 2024 model-angelo updated to version 1.0.13
ModelAngelo is an automatic atomic model building program for cryo-EM maps.
30 Nov 2024 biomodal updated to version 1.1.3
biomodal duet multiomics solution bioinformatics pipeline
29 Nov 2024 spaceranger updated to version 3.1.2
10x pipeline for processing Visium spatial RNA-seq data
27 Nov 2024 novasta updated to version 1.1
Installed with one user's request for their cryo-ET classification of the nuclear pore complex C++ version of subtomogram averaging (SA) scripts from TOM/AV3 package https://doi.org/10.1073/pnas.0409178102. Both CPU and GPU parallelization is supported although the latter performs significantly worse, build against CUDA10. Recommend the user to only cpus.
27 Nov 2024 cryosieve updated to version 1.2.8
CryoSieve is an advanced software solution designed for particle sorting/sieving in single particle analysis (SPA) for Cryogenic Electron Microscopy (cryo-EM).
27 Nov 2024 cryocare updated to version 0.3.0
Content-Aware Image Restoration for Cryo-Transmission Electron Microscopy Data: utilizes advanced image processing algorithms to enhance the quality of images obtained from Cryo-TEM (Cryo-Transmission Electron Microscopy) by selectively improving the contrast and detail of the important features within the image while minimizing noise, effectively making the data more interpretable for analysis, particularly in structural biology applications.
27 Nov 2024 surface_morphometrics updated to version 1.1
Surface_morphometrics: A pipeline of tools to generate robust open mesh surfaces from voxel segmentations of biological membranes using the Screened Poisson algorithm, calculate morphological features including curvature and membrane-membrane distance using pycurv's vector voting framework, and tools to convert these orphological quantities into morphometric insights.
26 Nov 2024 cryopros updated to version 1.0.0
CryoPROS is a computational framework specifically designed to tackle misalignment errors caused by preferred orientation issues in single-particle cryo-EM.
26 Nov 2024 alphapept updated to version 0.5.0
AlphaPept: a modern and open framework for MS-based proteomics
26 Nov 2024 nnUNet updated to version 2.4.2
nnU-Net is a PyTorch-based semantic segmentation application. It will analyze the provided training cases and automatically configure a matching U-Net-based segmentation pipeline.
26 Nov 2024 EDTA updated to version 2.2.2
The EDTA package was designed to filter out false discoveries in raw TE candidates and generate a high-quality non-redundant TE library for whole-genome TE annotations.
26 Nov 2024 lammps updated to version 29Aug2024
LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. It runs on a variety of different computer systems, including single processor systems, distributed-memory machines with MPI, and GPU and Xeon Phi systems. LAMMPS is open source software, released under the GNU General Public License.
25 Nov 2024 straglr updated to version 1.5.3
Tandem repeat expansion detection or genotyping from long-read alignments
22 Nov 2024 CADD updated to version 1.7.2
CADD (Combined Annotation Dependent Depletion) is a tool for scoring the deleteriousness of single nucleotide variants as well as insertion/deletions variants in the human genome. Currently, it supports the builds: GRCh37/hg19 and GRCh38/hg38.
19 Nov 2024 isoquant updated to version 3.6.2
IsoQuant is used to analyze long read RNA sequencing data
18 Nov 2024 cellranger updated to version 9.0.0
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.
18 Nov 2024 libjpeg-turbo updated to version 3.0.90
libjpeg-turbo is a JPEG image codec that uses SIMD instructions (MMX, SSE2, NEON) to accelerate baseline JPEG compression and decompression on x86, x86-64, and ARM systems.
18 Nov 2024 PMT (pb-metagenomics-tools) updated to version 2.1.0.
PB-metagenomics-tools is a suite of tools for performing metagenomic analyses using HiFi sequencing data. It comprises four pipelines: HiFi-MAG-Pipeline, Taxonomic-Profiling-Diamond-Megan, Taxonomic-Profiling-Minimap-Megan and Taxonomic-Profiling-Sourmash.
18 Nov 2024 steinbock updated to version 0.16.3
steinbock is a toolkit for processing multiplexed tissue images
16 Nov 2024 rgt updated to version 1.0.2
Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data. http://www.regulatory-genomics.org
15 Nov 2024 diann updated to version 1.9.2
DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing
15 Nov 2024 pychopper updated to version 2.7.10
Pychopper v2 is a tool to identify, orient and trim full-length Nanopore cDNA reads. The tool is also able to rescue fused reads.
14 Nov 2024 fastp updated to version 0.24.0
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.
13 Nov 2024 quast updated to version 5.3.0
QUAST stands for QUality ASsessment Tool. The tool evaluates genome assemblies by computing various metrics. The package includes the general QUAST tool for genome assemblies, MetaQUAST, the extension for metagenomic datasets, and Icarus, interactive visualizer for these tools.
8 Nov 2024 NAMD updated to version 3.0.1
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.
8 Nov 2024 R updated to version 4.4.2
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, ...).
8 Nov 2024 spiwalk updated to version 1.15.0
Simulates the behavior of spins under a specific # MR sequence within a microvascular network.
8 Nov 2024 uv updated to version 0.5.0
An extremely fast Python package and project manager, written in Rust.
7 Nov 2024 PhaseFinder updated to version 1.0-20240110
PhaseFinder detects DNA inversion mediated phase variation in bacterial genomes using genomic or metagenomic sequencing data. It works by identifying regions flanked by inverted repeats, mimicking their inversion in silico, and identifying regions where sequencing reads support both orientations.
7 Nov 2024 mriqc updated to version 24.0.2
MRIQC is an MRI quality control tool
7 Nov 2024 rseqc updated to version 5.0.4
Rseqc comprehensively evaluate RNA-seq datasets generated from clinical tissues or other well annotated organisms such as mouse, fly and yeast.
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