| Updated | Application
| 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 17 Nov 2025 | Genome Browser updated to version 490 | 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. 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. 12 Sep 2025 | antiSMASH updated to version 8.0.4 | antiSMASH allows the rapid genome-wide identification, annotation and analysis of secondary metabolite biosynthesis gene clusters in bacterial and fungal genomes. 12 Sep 2025 | proot updated to version 5.3.1 | PRoot is a user-space implementation of chroot 9 Sep 2025 | gubbins updated to version 3.4.3 | Gubbins is an algorithm that iteratively identifies loci containing elevated densities of base substitions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. 8 Sep 2025 | smrtanalysis updated to version 25.3 | 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. 4 Sep 2025 | datamash updated to version 1.9 | GNU datamash is a command-line program which performs basic numeric,textual and statistical operations on input textual data files. 3 Sep 2025 | hitips updated to version 1.1.4 | HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression. Documentations: https://hitips.readthedocs.io/en/latest/ 3 Sep 2025 | spIsoNet updated to version 1.0 | Single Particle spIsoNet (spIsoNet) is designed to correct for the preferred orientation problem in cryoEM by Self-supervised deep learning, by recovering missing information from well-sampled orientations in Fourier space. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data