| Updated | Application
| 15 Jun 2026 | famdb updated to version 3.0.0 | 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. 15 Jun 2026 | kneaddata updated to version 0.12.4 | KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments. 15 Jun 2026 | diamond updated to version 2.2.1 | DIAMOND is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity. 11 Jun 2026 | smrtanalysis updated to version 26.1 | 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. 11 Jun 2026 | bamtofastq updated to version 1.4.1 | Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis. 11 Jun 2026 | deepsomatic updated to version 1.10.0 | DeepSomatic is a google developed analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data. 11 Jun 2026 | TRsv updated to version 1.1.2 | Detection and Genotyping of Tandem Repeat Expansion/Contraction, Structural Variants (SVs), and Indels using Long Reads 11 Jun 2026 | MultAlin updated to version 5.4.1 | MultAlin creates a multiple sequence alignment from a group of related sequences using progressive pairwise alignments. 10 Jun 2026 | yass updated to version 1.16_alpha1 | yass is a genomic similarity seach tool for nucleic (and only nucleic) sequences in (multi)fasta or plain text format. yass produces local pairwise alignments in yass format, blast tabular format, or PSL format. 10 Jun 2026 | SvABA updated to version 2.0.20260514 | SvABA (formerly Snowman) is an SV and indel caller for short-read BAMs 10 Jun 2026 | sniffles updated to version 2.8.0 | 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. 10 Jun 2026 | gnomix updated to version 0-20260605 | G-Nomix does high resolution ancestry deconvolution for high-throughput sequencing data. 10 Jun 2026 | minimap2 updated to version 2.31 | 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). 9 Jun 2026 | exomiser updated to version 15.1.0 | The Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file. 8 Jun 2026 | sqanti3 updated to version 6.0.1 | Quality control of long-read transcriptomes. 8 Jun 2026 | novocraft updated to version 4.04.04 | 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. 8 Jun 2026 | hyperqueue updated to version 0.26.2 | 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. 5 Jun 2026 | aslprep updated to version 26.0.3 | Aslprep is an application for preprocessing of ASL (arterial spin labeling) data and computation of CBF (cerebral blood flow). Aslprep is a pipeline that uses AFNI, FSL, ANTs, and freesurfer. 3 Jun 2026 | alphafold3 updated to version 3.0.2 | This package provides an implementation of the inference pipeline of AlphaFold 3 3 Jun 2026 | ollama updated to version 0.30.2 | Ollama is a command line too that allows users to run LLMs locally. It can be used in many ways: interactive shell, API, Python library. It contains pre-built models that can be easily used in a variety of applications, including Llama4, Mistral and Gemma. Will use a GPU if there is one, otherwise will fallback to CPU. 1 Jun 2026 | nodejs updated to version 24.16.0 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 27 May 2026 | parallel updated to version 20260522 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 27 May 2026 | freebayes updated to version 1.3.10 | Bayesian haplotype-based polymorphism discovery and genotyping 22 May 2026 | dorado updated to version 2.0.0 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 22 May 2026 | SimNIBS updated to version 4.6.0 | SimNIBS is a free software package for the Simulation of Non-invasive Brain Stimulation. It allows for realistic calculations of the electric field induced by transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS). 22 May 2026 | stringtie updated to version 3.0.3 | 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. 21 May 2026 | sratoolkit updated to version 3.4.0 | The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format. 21 May 2026 | impute5 updated to version 1.2.0 | IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples. 20 May 2026 | isoquant updated to version 3.13.0 | IsoQuant is used to analyze long read RNA sequencing data 19 May 2026 | scanpy updated to version 1.12.1 | Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells. 18 May 2026 | apptainer updated to version 1.4.5 | Apptainer allows you to build and run Linux containers with emphasis on use in HPC. Apptainer is the Linux Foundation variant of Singularity. 15 May 2026 | modkit updated to version 0.6.2 | 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. 11 May 2026 | raxml-ng updated to version 2.0.1 | RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Successor to raxml. 7 May 2026 | clair3-rna updated to version 0.2.2 | Clair3-RNA is a small variant caller for long-read RNA sequencing (lrRNA-seq) data. Clair3-RNA supports ONT R10.4.1 and R9.4.1 complementary DNA sequencing (cDNA) and direct RNA sequencing (dRNA). Clair3-RNA also supports PacBio Sequel and PacBio MAS-Seq RNA sequencing data. 7 May 2026 | dragen_reports updated to version 4.4.4 | 6 May 2026 | PGAP updated to version 2026-04-27.build8516 | The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids). 5 May 2026 | deepvariant updated to version 1.10.0 | DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data. 5 May 2026 | sib-pair updated to version 1.00.beta | Sib-pair is a computer program for the manipulation and statistical analysis of genetic datasets. It implements analyses that can be applied to non-genetic data, such as generalized linear mixed models, multivariate survival analysis, log-linear modelling, conditional logistic regression, principal components analysis, polychoric and distance correlations, and a lot of mathematical distributions, eg multivariate normal, quadratic form of normals. 2 May 2026 | cellranger-arc updated to version 2.2.0 | 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. Furthermore, since the ATAC and gene expression measurements are on the very same cell, we are able to perform analyses that link chromatin accessibility and gene expression. 1 May 2026 | spaceranger updated to version 4.1.0 | 10x pipeline for processing Visium spatial RNA-seq data 30 Apr 2026 | remeta updated to version 0.11.1 | remeta is a collection of C++ programs for meta-analysis of single variants and gene-based tests using summary statistics from regenie. Installed from dockerfile of the GitHub repository. 30 Apr 2026 | AnnotSV updated to version 3.5.8 | AnnotSV is a program designed for annotating Structural Variations (SV). This tool compiles functionally, regulatory and clinically relevant information and aims at providing annotations useful to i) interpret SV potential pathogenicity and ii) filter out SV potential false positives. 29 Apr 2026 | brkraw updated to version 0.5.7 | The ‘BrkRaw’ is a python module designed to provide a comprehensive tool to access raw data acquired from Bruker Biospin preclinical MRI scanner. This module is also compatible with the zip compressed data to enable use of the archived data directly. The module is comprised of four components, including graphical user interface (GUI), command-line tools, high-level and low-level python APIs. 28 Apr 2026 | libreoffice updated to version 24.2.7 | Libreoffice is an open-source suite of office applications 27 Apr 2026 | multiqc updated to version 1.34 | aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report 27 Apr 2026 | DNAnexus updated to version 0.408.2 | 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. 21 Apr 2026 | trimgalore updated to version 0.6.11 | Consistent quality and adapter trimming for RRBS or standard FastQ files. 20 Apr 2026 | AutodockCrankprep updated to version 1.1 | "AutoDock CrankPep or ADCP is an AutoDock docking engine specialized for docking peptides. It combines technology form the protein folding filed with an efficient representation of a rigid receptor as affinity grids to fold the peptide in the context of the energy landscape created by the receptor." 15 Apr 2026 | Freesurfer updated to version 8.2.0 | 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. 15 Apr 2026 | RELION updated to version 5.1 | RELION (for REgularised LIkelihood OptimisatioN) is a stand-alone computer program for Maximum A Posteriori refinement of (multiple) 3D reconstructions or 2D class averages in cryo-electron microscopy. 15 Apr 2026 | zig updated to version 0.10.0 | Zig is a general-purpose programming language and toolchain for maintaining robust, optimal and reusable software. 14 Apr 2026 | Huygens updated to version 26.04 | 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. 10 Apr 2026 | fiberhmm updated to version 2.4.0 | HMM toolkit for calling chromatin footprints and MSPs from single-molecule data 9 Apr 2026 | IsoNet updated to version 2 | IsoNet is a deep learning-based software package that iteratively reconstructs the missing-wedge information and increases signal-to-noise ratio, using the knowledge learned from raw tomograms. Without the need for sub-tomogram averaging, IsoNet generates tomograms with significantly reduced resolution anisotropy. 8 Apr 2026 | fibertools updated to version 0.8.2 | Fiber-seq toolkit in rust 8 Apr 2026 | yes updated to version 0.8.2 | Fiber-seq toolkit in rust 6 Apr 2026 | xcp_d updated to version 26.0.2 | xcp_d is a postprocessing and noise regression pipeline for fMRI datasets (can use output from fmriprep and nibabies). 6 Apr 2026 | tedana updated to version 26.0.3 | Tedana is an application to denoise multi-echo fMRI datasets 3 Apr 2026 | rclone updated to version 1.73.3 | Rclone is a utility for synchronizing directories on a file-based storage system (e.g. /home or /data) with an object store such as Amazon S3. It uses the S3 protocol, and it can be used with the HPC object storage system. 31 Mar 2026 | gctb updated to version 2.5.5 | Genome-wide Complex Trait Bayesian analysis 31 Mar 2026 | liftoff updated to version 1.6.3 | Liftoff is a standalone tool that takes two genome assemblies and a reference annotation as input and outputs an annotation of the target genome. Liftoff uses Minimap2 to align the gene sequences from a reference genome to the target genome. Rather than aligning whole genomes, aligning only the gene sequences allows genes to be lifted over even if there are many structural differences between the two genomes. 31 Mar 2026 | PartekFlow updated to version 12.11.0 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 30 Mar 2026 | Matlab updated to version 2025a | 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. 30 Mar 2026 | fastp updated to version 1.3.1 | 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. 30 Mar 2026 | rust updated to version 1.94.0 | A language empowering everyone to build reliable and efficient software. 27 Mar 2026 | VirSorter2 updated to version 2.2.4 | VirSorter2 is a DNA and RNA virus identification tool. It leverages genome-informed database advances across a collection of customized automatic classifiers to improve the accuracy and range of virus sequence detection. 24 Mar 2026 | rMATS updated to version long-2.0.1 | MATS is a computational tool to detect differential alternative splicing events from RNA-Seq data. 23 Mar 2026 | Genome Browser updated to version 495 | 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. 19 Mar 2026 | codex updated to version 0.115.0 | Codex CLI is OpenAI’s coding agent that you can run locally from your terminal. It can read, change, and run code on your machine in the selected directory. It’s open source and built in Rust for speed and efficiency. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data