| Updated | Application
| 6 Jan 2026 | espresso updated to version 1.6.0 | ESPRESSO is a novel method for processing alignment of long read RNA-seq data, which can effectively improve splice junction accuracy and isoform quantification. ESPRESSO jointly considers alignments of all long reads aligned to a gene and uses error profiles of individual reads to improve the identification of splice junctions and the discovery of their corresponding transcript isoforms. 5 Jan 2026 | Maven updated to version 3.9.12 | Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. 5 Jan 2026 | parallel updated to version 20251222 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 30 Dec 2025 | sniffles updated to version 2.7.2 | 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. 23 Dec 2025 | ncbi-toolkit updated to version 29.8.0 | The NCBI C++ Toolkit is a set of executables and libraries for a multitude of sequence analysis functions. 22 Dec 2025 | sratoolkit updated to version 3.3.0 | The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format. 22 Dec 2025 | boost updated to version 1.90 | 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. 22 Dec 2025 | ncbi-datasets updated to version 18.13.0 | A one-stop shop for finding, browsing, and downloading genomic data. 20 Dec 2025 | Clair3 updated to version 1.2.0 | 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. 18 Dec 2025 | visidata updated to version 3.3 | VisiData is an interactive multitool for tabular data 18 Dec 2025 | alphalink2 updated to version 1.1.1 | alphalink2 is extended from AlphaLink for protein complexes predictions. AlphaLink2 is based on Uni-Fold and integrates crosslinking MS data directly into Uni-Fold. 18 Dec 2025 | zig updated to version 0.15.2 | Zig is a general-purpose programming language and toolchain for maintaining robust, optimal and reusable software. 17 Dec 2025 | boltzgen updated to version 0.2.0 | BoltzGen, an all-atom generative model for designing proteins and peptides across all modalities to bind a wide range of biomolecular targets. 17 Dec 2025 | snpEff updated to version 5.4a | snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes). 17 Dec 2025 | picard updated to version 3.4.0 | Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported. 16 Dec 2025 | rfantibody updated to version 94eb01f | RFantibody is an AI-based pipeline that designs antibody structures and sequences for a specified antigen epitope. 15 Dec 2025 | cellpose updated to version 4.0.8 | A generalist algorithm for cellular segmentation with human-in-the-loop capabilities. 15 Dec 2025 | macs updated to version 3.0.3 | Model-based Analysis of ChIP-Seq (MACS) on short reads sequencers such as Genome Analyzer (Illumina / Solexa). MACS empirically models the length of the sequenced ChIP fragments, which tends to be shorter than sonication or library construction size estimates, and uses it to improve the spatial resolution of predicted binding sites. MACS also uses a dynamic Poisson distribution to effectively capture local biases in the genome sequence, allowing for more sensitive and robust prediction. 15 Dec 2025 | iguane updated to version 9d6710c | IGUANe model for harmonization of MR images. 12 Dec 2025 | genometools updated to version 1.6.6 | collection of bioinformatic tools 11 Dec 2025 | nda-tools updated to version 0.2.26; 0.3.0; 0.5.0 | In order to submit data to the National Institute of Mental Health Data Archives (NDA), users must validate their data to ensure it complies with the required format. This is done using the NDA validation tool, vtcmd. Additionally, users can package and download data from NDA as well, using the downloadcmd tool. 11 Dec 2025 | SCENIC-plus updated to version 1.0.a2 | SCENIC+ is a new method for the inference of enhancer-driven gene regulatory networks (eGRN). It predicts genomic enhancers along with candidate upstream transcription factors (TF) and links these enhancers to candidate target genes. Specific TFs for each cell type or cell state are predicted based on the concordance of TF binding site accessibility, TF expression, and target gene expression. 10 Dec 2025 | novocraft updated to version 4.04.03 | 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. 10 Dec 2025 | subread updated to version 2.1.1 | High-performance read alignment, quantification and mutation discovery 10 Dec 2025 | clark updated to version 1.3.0.0 | A method based on a supervised sequence classification using discriminative k-mers 9 Dec 2025 | xpdf updated to version 4.06 | 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. 9 Dec 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. 9 Dec 2025 | cryosparc updated to version 4.7.1 | CryoSPARC (Cryo-EM Single Particle Ab-Initio Reconstruction and Classification) is a state of the art HPC software solution for complete processing of single-particle cryo-electron microscopy (cryo-EM) data. CryoSPARC is useful for solving cryo-EM structures of membrane proteins, viruses, complexes, flexible molecules, small particles, phase plate data and negative stain data. 9 Dec 2025 | Genome Browser updated to version 491 | 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. 3 Dec 2025 | MemXTerminator updated to version 1.2.2 | MemXTerminator is a software for membrane analysis and subtraction in cryo-EM. 2 Dec 2025 | cellranger updated to version 10.0.0 | 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. 1 Dec 2025 | modkit updated to version 0.6.0 | 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. 25 Nov 2025 | dorado updated to version 1.3.0 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 24 Nov 2025 | deepsomatic updated to version 1.9.0 | DeepSomatic is a google developed analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data. 20 Nov 2025 | nextflow updated to version 25.10.0 | Data-driven computational pipelines 18 Nov 2025 | PartekFlow updated to version 12.9.0 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 17 Nov 2025 | isoquant updated to version 3.10.0 | IsoQuant is used to analyze long read RNA sequencing data 14 Nov 2025 | cellranger-arc updated to version 2.1.0 | 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. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data