| Updated | Application
| 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. 29 Sep 2025 | parallel updated to version 20250922 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 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 | dorado updated to version 1.1.1 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 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. 15 Sep 2025 | sniffles updated to version 2.6.3 | 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. 15 Sep 2025 | Genome Browser updated to version 487 | 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. 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. 8 Sep 2025 | PartekFlow updated to version 12.8.0 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 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. 29 Aug 2025 | boltz updated to version 2.2.0 | Boltz is the state-of-the-art open-source model to predict biomolecular structures containing combinations of proteins, RNA, DNA, and other molecules. It also supports modified residues, covalent ligands and glycans, as well as conditioning the prediction on specified interaction pockets or contacts. 28 Aug 2025 | hisat updated to version 2.2.2.1-ngs3.2.1 | HISAT is a fast and sensitive spliced alignment program which uses Hierarchical Indexing for Spliced Alignment of Transcripts. 28 Aug 2025 | ncbi-ngs updated to version 3.2.1 | NCBI's NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing 28 Aug 2025 | ncbi-vdb updated to version 3.2.1 | The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. 27 Aug 2025 | roadies updated to version 0.1.10 | ROADIES is a fully automated pipeline to infer species trees starting from raw genome assemblies. It incorporates a unique strategy of randomly sampling segments of the input genomes to generate gene trees. This eliminates the need for predefining a set of loci, limiting the analyses to a fixed number of genes, and performing the cumbersome gene annotation and/or whole genome alignment steps. ROADIES also eliminates the need to infer orthology by leveraging existing discordance-aware methods that allow multicopy genes. 25 Aug 2025 | RepeatMasker updated to version 4.2.1 | 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. 18 Aug 2025 | CUDA updated to version 12.8 | CUDA is a parallel computing platform and programming model invented by NVIDIA. It enables dramatic increases in computing performance by harnessing the power of the graphics processing unit (GPU). Run 'module load CUDA' to access tools in CUDA. 7 Aug 2025 | dynamo updated to version 1.1.557 | Dynamo is a software environment for subtomogram averaging of cryo-EM data. 5 Aug 2025 | bismark updated to version 0.25.0 | Bismark is a program to map bisulfite treated sequencing reads to a genome of interest and perform methylation calls in a single step. The output can be easily imported into a genome viewer, such as SeqMonk, and enables a researcher to analyse the methylation levels of their samples straight away. 4 Aug 2025 | xcp_d updated to version 0.11.1 | xcp_d is a postprocessing and noise regression pipeline for fMRI datasets (can use output from fmriprep and nibabies). 1 Aug 2025 | fmriprep updated to version 25.1.4 | A Robust Preprocessing Pipeline for fMRI Data 30 Jul 2025 | minimap2 updated to version 2.30 | 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). 30 Jul 2025 | busco updated to version 6.0.0 | BUSCO completeness assessments employ sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB (www.orthodb.org) to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content. 29 Jul 2025 | gffcompare updated to version 0.12.10 | gffcompare can be used to compare and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie). It can collapse (merge) duplicate transcripts from multiple GTF/GFF3 files (e.g. resulted from assembly of different samples) and classify transcripts from one or multiple GTF/GFF3 files as they relate to reference transcripts provided in a annotation file (also in GTF/GFF3 format). 29 Jul 2025 | miniprot updated to version 0.18 | Miniprot aligns protein sequences to whole genomes with splicing and frameshift. It is primarily intended for annotating protein-coding genes in a new species using known genes from other species. 29 Jul 2025 | Freesurfer updated to version 8.1.0 | Freesurfer is a set of automated tools for reconstruction of the brain's cortical surface from structural MRI data, and overlay of functional MRI data onto the reconstructed surface. 28 Jul 2025 | mrtrix updated to version 3.0.7 | 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. 25 Jul 2025 | sRNAflow updated to version 20250717 | sRNAflow is a bioinformatic tool with a web interface designed for the analysis of small RNAs obtained from biological fluids. It allows filtering potential RNAs from reagents and environment, classifying small RNA types, managing small RNA annotation overlap, conducting differential expression assays, analysing isomiRs, and presenting an approach to identify the sources of small RNAs within samples. sRNAflow also supports an alternative alignment-free analysis of RNA-seq data, featuring clustering and initial RNA source identification using BLAST.diseases. 23 Jul 2025 | qsiprep updated to version 1.0.1 | qsiprep configures pipelines for processing diffusion-weighted MRI (dMRI) data. 22 Jul 2025 | unicycler updated to version 0.5.1 | Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. 21 Jul 2025 | ANTs updated to version 2.6.2 | 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. 21 Jul 2025 | celltypist updated to version 1.7.1 | CellTypist is an automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm. 21 Jul 2025 | AFNI updated to version 25.2.05 | 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. 18 Jul 2025 | BEAST updated to version 10.5.0,2.6.7 | BEAST (Bayesian Evolutionary Analysis Sampling Trees) is a cross-platform program for Bayesian MCMC analysis of molecular sequences. 17 Jul 2025 | parsnp updated to version 2.1.4 | Parsnp is a command-line-tool for efficient microbial core genome alignment and SNP detection. Parsnp was designed to work in tandem with Gingr, a flexible platform for visualizing genome alignments and phylogenetic trees 10 Jul 2025 | runme updated to version 3.14.2 | DevOps notebooks built with markdown 10 Jul 2025 | AR-Decon updated to version 0.9.0 | AR-Decon, which stands for correcting Anisotropic Resolution by Deconvolution, is a computational pipeline designed to enhance the quality of three-dimensional maps that suffer from anisotropic resolutions, often resulting from datasets with preferred orientations. 10 Jul 2025 | laynii updated to version 2.9.0 | Tools to analyze layer fMRI datasets 8 Jul 2025 | tortoisev4 updated to version 4.0.0 | 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 7 Jul 2025 | qupath updated to version 0.6.0 | QuPath is open source software for bioimage analysis. It is often used for digital pathology applications because it offers a powerful set of tools for working with whole slide images - but it can be applied to lots of other kinds of image as well. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data