| Updated | Application
| 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. 24 Nov 2025 | parallel updated to version 20251122 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 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 | sniffles updated to version 2.7.1 | 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. 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. 29 Sep 2025 | stripenn updated to version 1.1.65.20 | Stripenn is a command line interface python package developed for detection of atchitectural stripes from chromatin conformation capture (3C) data. It implements an algorithm rooted in computer vision for demarcation and quantification of the architectural stripes. Stripenn was demonstrated to outperform existing methods, be applicable in the context of analysis of B and T lymphocytes, and to allow examination of the role of sequence variation on the architectural stripes by studying the conservation of these features in inbred strains of mice. 24 Sep 2025 | nodejs updated to version 22.20.0 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 23 Sep 2025 | cactus updated to version 3.0.0 | Cactus is a reference-free whole-genome multiple alignment program. 16 Sep 2025 | wakhan updated to version 0.1.2 | Wakhan is a tool for analyzing chromosome-level changes in DNA using long reads from Oxford Nanopore or PacBio. It uses aligned long reads and phased variants to identify differences between haplotypes. The hapcorrect module corrects errors by using copy number differences. Wakhan also estimates the purity and ploidy of the sample and creates interactive plots showing haplotype-specific copy numbers and coverage. 16 Sep 2025 | severus updated to version 1.6 | Somatic structural variation caller for long reads (both PacBio and ONT). 15 Sep 2025 | ollama updated to version 0.11.8 | 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. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data