Application updates in the last 3 months
To see all versions available for any application, use module avail application_nameAll centrally-installed applications are listed on the Applications page
| Updated | Application |
| 13 Mar 2025 | miniprot updated to version 0.14 Miniprot aligns protein sequences to whole genomes with splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. |
| 13 Mar 2025 | smrtanalysis updated to version 25.2 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. |
| 13 Mar 2025 | sniffles updated to version 2.6.1 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. |
| 13 Mar 2025 | gubbins updated to version 3.4 Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. |
| 13 Mar 2025 | BindCraft updated to version 1.5.0 BindCraft is an open-source and automated pipeline for de novo protein binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. |
| 13 Mar 2025 | Freesurfer updated to version 8.0.0 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. |
| 12 Mar 2025 | PEPATAC updated to version 0.12.2 PEPATAC is a robust pipeline for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) built on a loosely coupled modular framework. It may be easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. It is optimized on unique features of ATAC-seq data to be fast and accurate and provides several unique analytical approaches. |
| 10 Mar 2025 | R updated to version 4.4.3 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, ...). |
| 7 Mar 2025 | deepict updated to version 1.0.0 DeePiCt (Deep Picker in Context), a deep-learning based pipeline to achieve structure segmentation and particle localization in cryo-electron tomography. DeePiCt combines two dedicated convolutional networks: a 2D CNN for segmentation of cellular compartments (e.g. organelles or cytosol), and a 3D CNN for particle localization and structure segmentation. |
| 6 Mar 2025 | VEP updated to version 113 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. |
| 6 Mar 2025 | deeptools updated to version 3.5.6 deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing DNA sequencing experiments. |
| 6 Mar 2025 | csvkit updated to version 2.1.0 csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. |
| 5 Mar 2025 | SQLite updated to version 3.49.1 SQLite is a software library that implements a self-contained, serverless, zero-configuration, transactional SQL database engine. |
| 5 Mar 2025 | diann updated to version 2.0.2 DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing |
| 3 Mar 2025 | rdfind updated to version 1.7.0 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. |
| 3 Mar 2025 | sodium updated to version 1.0.20 Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing, and more. |
| 3 Mar 2025 | SciTE updated to version 5.5.5 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. |
| 3 Mar 2025 | EDirect updated to version 23.5.20250228 Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. |
| 28 Feb 2025 | spaceranger updated to version 3.1.3 10x pipeline for processing Visium spatial RNA-seq data |
| 28 Feb 2025 | cellranger updated to version 9.0.1 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. |
| 27 Feb 2025 | sirvsuite updated to version 0.1.3 QC tool for RNA-Seq workflow using Lexogen's SIRV spike-in controls |
| 25 Feb 2025 | alphafold3 updated to version 3.0.1 This package provides an implementation of the inference pipeline of AlphaFold 3 |
| 25 Feb 2025 | uv updated to version 0.6.3 An extremely fast Python package and project manager, written in Rust. |
| 24 Feb 2025 | cactus updated to version 2.9.3 Cactus is a reference-free whole-genome multiple alignment program. |
| 24 Feb 2025 | zstd updated to version 1.5.7 Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios. |
| 24 Feb 2025 | parallel updated to version 20250222 GNU parallel is a shell tool for executing jobs in parallel using one or more computers. |
| 23 Feb 2025 | PartekFlow updated to version 12.4.2 Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. |
| 21 Feb 2025 | hyperqueue updated to version 0.21.1 HyperQueue (HQ) lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups tasks into SLURM/PBS jobs and distributes them to fully utilize allocated nodes. |
| 20 Feb 2025 | bwulf updated to version 0.3.1 unified interface to custom utilities by the NIH HPC staff. |
| 19 Feb 2025 | gromacs updated to version 2024.4 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. |
| 14 Feb 2025 | vg updated to version 1.63.1 Tools for working with genome variation graphs |
| 13 Feb 2025 | MUMmer updated to version 4.0.1 Mummer is a system for aligning entire genomes extremely rapidly. |
| 13 Feb 2025 | fraposa updated to version 032123 Fraposa predicts the ancestry of study samples by using principle component analysis (PCA) with a reference panel. |
| 11 Feb 2025 | AlphaPulldown updated to version 2.0.1 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. |
| 10 Feb 2025 | hitips updated to version 1.0.12 HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression. Documentations: https://hitips.readthedocs.io/en/latest/ |
| 10 Feb 2025 | esm updated to version 3.1.2 Code and pre-trained weights for Transformer protein language models from the Meta Fundamental AI Research Protein Team (FAIR) |
| 5 Feb 2025 | marp updated to version 4.1.1 A CLI for Marp and any slide deck converter based on Marpit framework. It can convert Marp / Marpit Markdown files into static HTML / CSS, PDF, PowerPoint document, and image(s) easily. |
| 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). |
| 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. |
| 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 | 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:
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| 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 | 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. |
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