| Updated | Application
| 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. 18 Aug 2025 | Genome Browser updated to version 485 | 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 Aug 2025 | parallel updated to version 20250722 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 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. 3 Jul 2025 | LAST updated to version 1642 | LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:
2 Jul 2025 | sqanti3 updated to version 5.5 | Quality control of long-read transcriptomes. 1 Jul 2025 | sqanti-sim updated to version 4b139e7 | long-read RNA-seq (LRS) simulation tool 26 Jun 2025 | cryocat updated to version 0.6.1 | Contextual Analysis Tools for cryoET and subtomogram averaging, prepossessing step for gapstop: 25 Jun 2025 | seqtk updated to version 1.5 | seqtk is a toolkit for processing sequences in FASTA/Q formats 25 Jun 2025 | diamond updated to version 2.1.12 | DIAMOND is a new high-throughput program for aligning DNA reads or protein sequences against a protein reference database such as NR, at up to 20,000 times the speed of BLAST, with high sensitivity. 23 Jun 2025 | PartekFlow updated to version 12.7.0 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 20 Jun 2025 | bcl-convert updated to version 4.2.7 | The Illumina BCL Convert is a standalone local software app that converts the Binary Base Call (BCL) files produced by Illumina sequencing systems to FASTQ files. BCL Convert also provides adapter handling (through masking and trimming) and UMI trimming and produces metric outputs. 17 Jun 2025 | ollama updated to version 0.9.1 | 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. 17 Jun 2025 | spaceranger updated to version 4.0.1 | 10x pipeline for processing Visium spatial RNA-seq data 17 Jun 2025 | camus updated to version 0.1 | Fitting and denovo imputation of cancer mutational signature 12 Jun 2025 | dcm2niix updated to version 1.0.20250506 | DICOM to NIfTI converter 12 Jun 2025 | boltz updated to version 2.1.1 | 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. 12 Jun 2025 | connectome-workbench updated to version 2.1.0 | Tools to browse, download, explore, and analyze data from the Human Connectome Project (HCP). Allows users to compare their own data to that of the HCP. 12 Jun 2025 | tedana updated to version 25.0.1 | Tedana is an application to denoise multi-echo fMRI datasets 10 Jun 2025 | famdb updated to version 2.0.2 | FamDB is a modular HDF5-based export format and query tool developed for offline access to the Dfam database of transposable element and repetitive DNA families. 9 Jun 2025 | netcdf updated to version 4.9.3 | NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. 9 Jun 2025 | SciTE updated to version 5.5.7 | 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. 4 Jun 2025 | deepmod2 updated to version 0.3.1 | Tool for detecting DNA 5mC methylation from Oxford Nanopore reads. 4 Jun 2025 | Bsoft updated to version 2.4.0 | Bsoft is a collection of programs and a platform for development of software for image and molecular processing in structural biology. Problems in structural biology are approached with a highly modular design, allowing fast development of new algorithms without the burden of issues such as file I/O. It provides an easily accessible interface, a resource that can be and has been used in other packages. 2 Jun 2025 | rstudio-server updated to version 2025.05.0-496 | RStudio Server is a web-based R IDE similar to RStudio Desktop. 29 May 2025 | Tractor updated to version 1.4.0 | Tractor is a statistical framework and software package to facilitate the inclusion of admixed individuals in association studies by leveraging local ancestry. It generates accurate ancestry-specific effect-size estimates and P values, can boost genome-wide association study (GWAS) power and improves the resolution of association signals 29 May 2025 | fastp updated to version 0.24.3 | A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. 28 May 2025 | apptainer updated to version 1.3.6 | Apptainer allows you to build and run Linux containers with emphasis on use in HPC. Apptainer is the Linux Foundation variant of and successor to the widely popular Singularity. 27 May 2025 | boost updated to version 1.88 | 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. 27 May 2025 | dorado updated to version 1.0.0 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data