| Updated | Application
| 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. 23 Jun 2025 | fmriprep updated to version 25.1.3 | A Robust Preprocessing Pipeline for fMRI Data 23 Jun 2025 | parallel updated to version 20250622 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 23 Jun 2025 | Genome Browser updated to version 483 | 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. 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 17 Jun 2025 | AFNI updated to version 25.1.15 | 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. 12 Jun 2025 | dcm2niix updated to version 1.0.20250506 | DICOM to NIfTI converter 12 Jun 2025 | ANTs updated to version 2.6.1 | 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. 12 Jun 2025 | boltz updated to version 2.1.1 | Boltz-1 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. 22 May 2025 | FSL updated to version 6.0.7.18 | FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. 22 May 2025 | modkit updated to version 0.5.0 | 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. 21 May 2025 | bamtools updated to version 2.5.3 | BamTools provides a fast, flexible C++ API & toolkit for reading, writing, and manipulating BAM files. 21 May 2025 | nextflow updated to version 25.04.2 | Data-driven computational pipelines 21 May 2025 | shasta updated to version 0.14.0 | De novo assembly from Oxford Nanopore reads 20 May 2025 | FaceAge updated to version 1.0 | FaceAge is a deep learning system to estimate biological age from easily obtainable and low-cost face photographs. FaceAge was trained on data from 58 851 presumed healthy individuals aged 60 years or older. 20 May 2025 | Huygens updated to version 25.04 | Huygens is an image restoration, deconvolution, resolution and noise reduction. It can process images from all current optical microscopes, including wide-field, confocal, Nipkow (scanning disk confocal), multiple-photon, and 4Pi microscopes. 16 May 2025 | Python updated to version 3.12 | Python is a programming language that lets you work more quickly and integrate your systems more effectively. 14 May 2025 | rust updated to version 1.86.0 | A language empowering everyone to build reliable and efficient software. 13 May 2025 | mrtrix updated to version 3.0.5 | 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 May 2025 | RepeatMasker updated to version 4.1.9 | 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. 12 May 2025 | Rstudio updated to version 2024.12.0-467 | RStudio is a set of integrated tools designed to help you be more productive with R. It includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management. 8 May 2025 | Lmod updated to version 8.7.60 | Lmod Environment Module system from TACC 1 May 2025 | ctat_lr_fusion updated to version 1.1.0 | Find fusion transcripts using minimap2 and FusionInspector for long RNA-seq reads. 29 Apr 2025 | rapidtide updated to version 2.8.2; 3.0.2 | Rapidtide is a suite of Python programs used to model, characterize, visualize, and remove time varying, physiological blood signals from fMRI and fNIRS datasets. The primary workhorses of the package are the rapidtide program, which characterizes bulk blood flow, and happy, which focusses on the cardiac band. 29 Apr 2025 | util-linux updated to version 2.4.1 | Random collection of linux utilities. 29 Apr 2025 | isoseqsim updated to version 0.2 | Simulates Iso-Seq reads for evaluating the performance of Iso-Seq bioinformatics analysis tools. 23 Apr 2025 | hicexplorer updated to version 3.7.6 | Tools to process, normalize and visualize Hi-C data 23 Apr 2025 | xcp_d updated to version 0.10.7 | xcp_d is a postprocessing and noise regression pipeline for fMRI datasets (can use output from fmriprep and nibabies). 22 Apr 2025 | MuSE updated to version 2.1.2 | MuSE is an approach to somatic variant calling based on the F81 Markov substitution model for molecular evolution, which models the evolution of the reference allele to the allelic composition of the matched tumor and normal tissue at each genomic locus. 22 Apr 2025 | datalad updated to version 1.1.4 | Datalad is a tool for uploading and downloading public up-t-to-date neuroimaging datasets. 22 Apr 2025 | hifiasm updated to version 0.25.0 | Hifiasm is a fast haplotype-resolved de novo assembler initially designed for PacBio HiFi reads. Its latest release supports telomere-to-telomere assembly by utilizing ultralong Oxford Nanopore reads. It can produce better haplotype-resolved assemblies when given parental short reads or Hi-C data. 22 Apr 2025 | mandalorion updated to version 4.5 | Mandalorion is a pipeline to identify isoforms from full-length cDNA sequencing data. 21 Apr 2025 | pggb updated to version 0.7.3 | pangenome graph builder. 21 Apr 2025 | sniffles updated to version 2.6.2 | 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. 21 Apr 2025 | minimap2 updated to version 2.29 | 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). 21 Apr 2025 | miniprot updated to version 0.15 | 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. 21 Apr 2025 | Julia updated to version 1.11.5 | high level, dynamic language for technical computing 14 Apr 2025 | cellpose updated to version 3.1.1 | A generalist algorithm for cellular segmentation with human-in-the-loop capabilities. 14 Apr 2025 | extrautils updated to version 1.0 | Extra command line utilities not available by default, all in one convenient location, as simple as module load extrautils. 14 Apr 2025 | neovim updated to version 0.11.0 | Neovim is a refactor, and sometimes redactor, in the tradition of Vim (which itself derives from Stevie). It is not a rewrite but a continuation and extension of Vim. 11 Apr 2025 | cactus updated to version 2.9.7 | Cactus is a reference-free whole-genome multiple alignment program. 11 Apr 2025 | chopper updated to version 0.9.2 | Filtering and trimming for long-read sequencing data (PacBio/ONT). 11 Apr 2025 | whatshap updated to version 2.5 | WhatsHap is a software for phasing genomic variants using DNA sequencing reads, also called read-based phasing or haplotype assembly. It is especially suitable for long reads, but works also well with short reads. 11 Apr 2025 | trgt updated to version 2.0.0 | TRGT is a tool for targeted genotyping of tandem repeats from PacBio HiFi data. In addition to the basic size genotyping, TRGT profiles sequence composition, mosaicism, and CpG methylation of each analyzed repeat. TRGT can also create a visualization of reads overlapping the repeats. 10 Apr 2025 | laynii updated to version 2.8.0 | Tools to analyze layer fMRI datasets 9 Apr 2025 | Mathematica updated to version 14.2.1 | Mathematica is an interactive system for doing mathematical computation. It performs numerical, symbolic and graphical computations, and incorporates a high-level programming language. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data