| Updated | Application
| 27 Aug 2026 | totalsegmentator updated to version 2.18.0 | TotalSegmentator is a command-line tool that automatically identifies and outlines anatomical structures in CT and MRI scans. It can create separate labeled images for organs, bones, muscles, blood vessels, and other parts of the body. 27 Aug 2026 | texinfo updated to version 7.3 | Texinfo is the official documentation format of the GNU project 26 Aug 2026 | halfpipe updated to version 1.3.2 | HALFpipe is a workflow for analyzing resting-state and task-based fMRI data. It supports preprocessing, individual participant analysis, and group analysis, and it can work with datasets that have not already been converted to BIDS format. HALFpipe combines methods from established neuroimaging tools, including fMRIPrep, ANTs, FreeSurfer, FSL, AFNI, and Nipype, to provide a consistent and reproducible analysis process. 26 Aug 2026 | fmripost-aroma updated to version 0.0.12 | fMRIPost-AROMA is a workflow for reducing motion-related noise in fMRI data that have already been preprocessed. It uses ICA-AROMA and works with BIDS-formatted derivatives, including compatible outputs from fMRIPrep, as long as the BOLD images are in MNI152NLin6Asym space at 2 mm resolution. It replaces the ICA-AROMA workflow that was included in fMRIPrep version 23.0 and earlier. 26 Aug 2026 | PartekFlow updated to version 12.11.2 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 25 Aug 2026 | hic_qc updated to version 1.2 | hic_qc.py is a command-line tool for checking the quality of Hi-C sequencing libraries using reads aligned to a reference genome or assembly. It measures long-range contacts, contacts between contigs, mapping quality, duplicate reads, and the distribution of distances between read pairs. The tool produces summary statistics, plots, and an optional report that can help identify weak Hi-C signal or possible problems with the library or assembly. 24 Aug 2026 | SciTE updated to version 5.6.6 | 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. 24 Aug 2026 | micapipe updated to version 0.2.3 | Micapipe is a workflow for processing multiple types of brain MRI data, including structural, diffusion, resting-state functional, and microstructure-sensitive imaging. It takes data organized in BIDS format and produces standardized maps and connectivity measures that researchers can use to study brain structure and function across different regions and spatial scales. 21 Aug 2026 | smrtanalysis updated to version 26.2 | 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. 21 Aug 2026 | qsirecon updated to version 26.0.0 | QSIRecon is a post-processing workflow for diffusion MRI data. It takes data that have already been preprocessed, usually with QSIPrep, and applies reconstruction and analysis methods from tools such as MRtrix3, DIPY, DSI Studio, and PyAFQ. Depending on the selected workflow, it can fit diffusion models, estimate fiber orientations, generate tractography, measure properties along white-matter pathways, and create regional connectivity tables. It provides standardized, reproducible workflows so researchers do not have to assemble every analysis step themselves. 20 Aug 2026 | biomodal updated to version 2.1.0 | biomodal duet multiomics solution bioinformatics pipeline 19 Aug 2026 | Genome Browser updated to version 502 | 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. 18 Aug 2026 | mricrogl updated to version 1.2.20220720 | MRIcroGL is a cross-platform application for viewing and exploring neuroimaging data. It displays images as 2D slices or interactive 3D renderings and can combine anatomical scans with functional or statistical overlays. MRIcroGL supports common imaging formats, including NIfTI and DICOM, and provides both a graphical interface and scripting tools for creating reproducible visualizations. 10 Aug 2026 | salmon updated to version 2.5.0 | a tool for quantifying the expression of transcripts using RNA-seq data. 10 Aug 2026 | ollama updated to version 0.32.7 | 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. 7 Aug 2026 | mvapich updated to version 4.1 | MPI implementation for Infiniband 4 Aug 2026 | connectome-workbench updated to version 2.2.1 | Tools to browse, download, explore, and analyze data from the Human Connectome Project (HCP). Allows users to compare their own data to that of the HCP. 4 Aug 2026 | rfd3 updated to version 0.2.0 | RFD3 (RFdiffusion3) uses an atom-level diffusion framework to design proteins around ligands, nucleic acids, and other nonprotein molecular components. Because it generates complete atomic structures rather than only protein backbones, it can incorporate detailed geometric constraints for applications such as enzyme engineering and the design of proteins that bind small molecules or DNA. 3 Aug 2026 | dorado updated to version 2.1.1 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 28 Jul 2026 | NAMD updated to version 3.0.2 | 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. 27 Jul 2026 | LAST updated to version 1652 | LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:
24 Jul 2026 | sqanti3 updated to version 6.0.2 | Quality control of long-read transcriptomes. 24 Jul 2026 | jvarkit updated to version 20260430 | Java tools for bioinformatics 23 Jul 2026 | eggNOG-mapper updated to version 2.1.15 | eggNOGmapper is a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database. Orthology assignment is ideally suited for functional inference. However, predicting orthology is computationally intensive at large scale, and most other pipelines are relatively inaccessible (e.g., new assignments only available through database updates), so less precise homology-based functional transfer was previously the default for (meta-)genome annotation. 23 Jul 2026 | tomoDRGN updated to version v1.0.4 | TomoDRGN extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles. For cryo-ET samples imaging particles in situ, tomoDRGN therefore enables continuous heterogeneity analysis at a single particle level within the native cellular environment. 23 Jul 2026 | petprep updated to version 0.0.8 | Pre-processing of PET datasets: Motion correction, segment anatomy, registration, volume correction, generation of quality reports, and others using tools from several neuroimaging applications such as FSL, ANTs, freesurfer, AFNI. 22 Jul 2026 | Clair3 updated to version 2.0.2 | Clair3 is a small variant caller for Illumina, PacBio and ONT long reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster. 22 Jul 2026 | parallel updated to version 20260722 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 22 Jul 2026 | Meryl updated to version 1.4.2 | Meryl: a genomic k-mer counter (and sequence utility) with nice features. It is built into the Celera Assembler and is also available as a stand-alone application. Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order. 21 Jul 2026 | whatshap updated to version 2.8 | 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. 21 Jul 2026 | augustus updated to version 3.5.0 | AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. 21 Jul 2026 | rmblast updated to version 2.17.1 | 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. 21 Jul 2026 | preseq updated to version 3.2.0 | predicting library complexity and genome coverage in high-throughput sequencing 20 Jul 2026 | RepeatMasker updated to version 4.2.4 | 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. 17 Jul 2026 | merqury updated to version 1.4.1 | Evaluate genome assemblies with k-mers and more 16 Jul 2026 | baysor updated to version 0.8.2 | 15 Jul 2026 | mbg updated to version 1.0.17 | Minimizer based sparse de Bruijn Graph constructor. 15 Jul 2026 | kallisto updated to version 0.52.0 | kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment. 15 Jul 2026 | plink updated to version 7.1-alpha | PLINK is whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. 15 Jul 2026 | spades updated to version 4.3.0 | SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies. 15 Jul 2026 | PAML updated to version 4.10.10 | A package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood. 10 Jul 2026 | sicer updated to version 2.1.1 | A clustering approach for identification of enriched domains from histone modification ChIP-Seq data 7 Jul 2026 | cellranger updated to version 10.1.0 | 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. 6 Jul 2026 | Perl updated to version 5.42 | Perl is a highly capable, feature-rich programming language with over 30 years of development. 2 Jul 2026 | boost updated to version 1.91 | 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. 30 Jun 2026 | abyss updated to version 2.3.10 | Abyss represents Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. The parallel version is implemented using MPI and is capable of assembling larger genomes. 30 Jun 2026 | csvkit updated to version 2.2.0 | csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. 29 Jun 2026 | clark updated to version 1.4.5.0-a | A method based on a supervised sequence classification using discriminative k-mers 29 Jun 2026 | circos updated to version 0.69-10 | Circos is a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. Also, Circos is useful to visualize any type of information that benefits from a circular layout. Thus, although it has been designed for the field of genomics, it is sufficiently flexible to be used in other data domains. 29 Jun 2026 | agat updated to version 1.7.0 | Another Gtf/Gff Analysis Toolkit 29 Jun 2026 | cnvkit updated to version 0.9.13 | Copy number variant detection from targeted DNA sequencing 29 Jun 2026 | rust updated to version 1.96.0 | A language empowering everyone to build reliable and efficient software. 26 Jun 2026 | trimgalore updated to version 2.2.0 | Consistent quality and adapter trimming for RRBS or standard FastQ files. 24 Jun 2026 | htseq updated to version 2.1.2 | HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays. 24 Jun 2026 | bowtie2 updated to version 2.5.5 | 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 23 Jun 2026 | RevBayes updated to version 1.4.0 | Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language 22 Jun 2026 | vcfanno updated to version 0.3.9 | annotate a VCF with other VCFs/BEDs/tabixed files 22 Jun 2026 | nodejs updated to version 24.17.0 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 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 | 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 | 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 |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data