| Updated | Application
| 15 Mar 2026 | PartekFlow updated to version 12.10.0 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 12 Mar 2026 | singularity updated to version 4.3.7 | Singularity is a container platform focused on supporting ``Mobility of Compute``. It allows users to emulate, and share custom Linux environments allowing for the creation of self-contained development stacks. 11 Mar 2026 | STAR-Fusion updated to version 1.15.1 | Transcript fusion detection 9 Mar 2026 | Clair3 updated to version 2.0.0 | 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. 6 Mar 2026 | samtools updated to version 1.23 | The samtools package now provides samtools, bcftools, tabix, and the underlying htslib library. 6 Mar 2026 | GATK updated to version 4.6.2.0 | GATK, from the Broad Institute, is a structured software library that makes writing efficient analysis tools using next-generation sequencing data very easy, and second it's a suite of tools for working with human medical resequencing projects such as 1000 Genomes and The Cancer Genome Atlas. These tools include things like a depth of coverage analyzers, a quality score recalibrator, a SNP/indel caller and a local realigner. 6 Mar 2026 | seqkit updated to version 2.13.0 | A cross-platform toolkit for FASTA/Q file manipulation 3 Mar 2026 | telomerehunter2 updated to version 1.0.6 | 3 Mar 2026 | kanpig updated to version 2.0.2 | A fast tool for genotyping structural variants with long-reads 2 Mar 2026 | ollama updated to version 0.17.5 | 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. 2 Mar 2026 | rdfind updated to version 1.8.0 | 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. 2 Mar 2026 | SciTE updated to version 5.6.0 | 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. 2 Mar 2026 | Genome Browser updated to version 494 | 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. 2 Mar 2026 | libfreetype updated to version 2.14.2 | FreeType is a freely available software library to render fonts. 27 Feb 2026 | libwebp updated to version 1.6.0 | WebP codec is a library to encode and decode images in WebP format. This package contains the library that can be used in other programs to add WebP support, as well as the command line tools ‘cwebp’ and ‘dwebp’ to compress and decompress images respectively 26 Feb 2026 | mirp updated to version 2 | Microtubule Image Processing in RELIONv3.1 Pipeline. 26 Feb 2026 | Cytoscape updated to version 3.10.4 | Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. 26 Feb 2026 | cellranger-atac updated to version 2.2.0 | Cell Ranger ATAC is a set of analysis pipelines that process Chromium Single Cell ATAC data. 23 Feb 2026 | parallel updated to version 20260222 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 18 Feb 2026 | cooltools updated to version 0.7.1 | Cooltools is a suite of computational tools that enables flexible, scalable, and reproducible analysis of high-resolution contact frequency data. Cooltools leverages the widely-adopted cooler format which handles storage and access for high-resolution datasets. Cooltools provides a paired command line interface and Python application programming interface, which respectively facilitate workflows on high-performance computing clusters and in interactive analysis environments. 17 Feb 2026 | qgrs updated to version 1.0 | QGRS, a pattern in DNA or RNA that can fold into a "G-quadruplex"—a four-stranded structure. These structures are built from "tetrads"(groups of 4 Guanine molecules). This program differs from the actual algorithm used by QGRS Mapper server regarding overlapping motifs and the maximum length of the motifs. 12 Feb 2026 | Autodock-GPU updated to version 1.6 | Autodock-GPU performs docking calculations, and processes ligand-receptor poses in parallel over multiple compute units on GPUs. 10 Feb 2026 | tortoisev4 updated to version 4.1.0 | TORTOISE (Tolerably Obsessive registration and Tensor Optimization Indolent Software Ensemble) is a suite of programs for for pre-processing, post-processing and analyzing diffusion MRI data 9 Feb 2026 | ANNOVAR updated to version 2025-03-02 | ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes. 5 Feb 2026 | straglr updated to version 1.5.6 | Tandem repeat expansion detection or genotyping from long-read alignments 30 Jan 2026 | AFNI updated to version 26.0.08 | AFNI (Analysis of Functional NeuroImages) is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. 27 Jan 2026 | repeatmodeler updated to version 2.0.7 | RepeatModeler is a de novo transposable element (TE) family identification and modeling package. RepeatModeler assists in automating the runs of the various algorithms given a genomic database, clustering redundant results, refining and classifying the families and producing a high quality library of TE families suitable for use with RepeatMasker and ultimately for submission to the Dfam database (http://dfam.org). 27 Jan 2026 | Eigen updated to version 5.0.0 | Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. 26 Jan 2026 | cutadapt updated to version 5.2 | 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. 16 Jan 2026 | fcs updated to version 0.5.5 | FCS is a toolset to remove contaminant sequences from a genome assembly. 16 Jan 2026 | RGI updated to version 6.0.5 | RGI (Resistance Gene Identifier) is a robust antimicrobial resistance (AMR) gene predicting tool. It is based on newly curated Comprehensive Antibiotic Research Database (CARD) and allows detection detect AMR genes from thirteen genomes of Pseudomonas strains. 15 Jan 2026 | fmriprep updated to version 25.2.4 | A Robust Preprocessing Pipeline for fMRI Data 15 Jan 2026 | ANTs updated to version 2.6.5 | Advanced Normalization Tools (ANTs) extracts information from complex datasets that include imaging. Paired with ANTsR (answer), ANTs is useful for managing, interpreting and visualizing multidimensional data. 15 Jan 2026 | diann updated to version 1.9.2 | DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing 13 Jan 2026 | tedana updated to version 25.1.0 | Tedana is an application to denoise multi-echo fMRI datasets 13 Jan 2026 | Mathematica updated to version 14.3.0 | Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language. 13 Jan 2026 | mrtrix updated to version 3.0.8 | MRtrix provides a large suite of tools for image processing, analysis and visualisation, with a focus on the analysis of white matter using diffusion-weighted MRI. 12 Jan 2026 | xcp_d updated to version 0.14.0 | xcp_d is a postprocessing and noise regression pipeline for fMRI datasets (can use output from fmriprep and nibabies). 12 Jan 2026 | bwulf updated to version 0.4 | unified interface to custom utilities by the NIH HPC staff. 9 Jan 2026 | gtdb-tk updated to version 2.6.1 | GTDB-Tk is a software toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes based on the Genome Database Taxonomy 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. 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. 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. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data