| Updated | Application
| 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 20 Apr 2025 | PartekFlow updated to version 12.5.1 | Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing. 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 10 Apr 2025 | AFNI updated to version 25.1.01 | 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. 10 Apr 2025 | FSL updated to version 6.0.7.17 | FSL is a comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data. 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. 8 Apr 2025 | dorado updated to version 0.9.5 | Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads. 8 Apr 2025 | ANTs updated to version 2.6.0 | 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. 4 Apr 2025 | OpenStructure updated to version 2.9.2 | Open-Source Computational Structural Biology Framework 4 Apr 2025 | xcp_d updated to version 0.10.6 | xcp_d is a postprocessing and noise regression pipeline for fMRI datasets (can use output from fmriprep and nibabies). 3 Apr 2025 | fmriprep updated to version 25.0.0 | A Robust Preprocessing Pipeline for fMRI Data 2 Apr 2025 | RepeatMasker updated to version 4.1.8 | 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. 2 Apr 2025 | vmd updated to version 2.0.0a5 | VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. To use, type vmd at the prompt. 1 Apr 2025 | sratoolkit updated to version 3.2.1 | The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format. 31 Mar 2025 | singularity updated to version 4.2.2 | Singularity is a container platform focused on supporting ``Mobility of Compute``. It allows users to emulate, and share custom Linux environments allowing for the creation of self-contained development stacks. 28 Mar 2025 | parallel updated to version 20250322 | GNU parallel is a shell tool for executing jobs in parallel using one or more computers. 27 Mar 2025 | idc-index updated to version 0.8.2 | idc-index is a Python package that enables basic operations for working with NCI Imaging Data Commons (IDC): https://portal.imaging.datacommons.cancer.gov/ 26 Mar 2025 | multiqc updated to version 1.28 | aggregates results for various frequently used bioinformatics tools across multiple samples into a nice visual report 24 Mar 2025 | Xplor-NIH updated to version 3.10 | Xplor-NIH is a structure determination program which builds on the X-PLOR v3.851 program, including additional tools developed at the NIH. 24 Mar 2025 | synapseclient updated to version 4.7.0 | The synapseclient package provides an interface to Synapse, a collaborative workspace for reproducible, data intensive research projects 21 Mar 2025 | qsiprep updated to version 1.0.0 | qsiprep configures pipelines for processing diffusion-weighted MRI (dMRI) data. 21 Mar 2025 | parabricks updated to version 4.5.0 | The Clara Parabricks toolkit is a set of GPU-accelerated genome analysis tools for secondary analysis of next generation sequencing data. 20 Mar 2025 | AlphaPulldown updated to version 2.0.2 | AlphaPulldown is a Python package that streamlines protein-protein interaction screens and high-throughput modelling of higher-order oligomers using AlphaFold-Multimer. It provides a convenient command-line interface, a variety of confidence scores and a graphical analysis tool. 20 Mar 2025 | ProteinMPNN updated to version 1.0.1 | ProteinMPNN is a deep learning–based protein sequence design method. Unlike AlphaFold and Rosettafold, which both predict protein structures from sequence, ProteinMPNN tries to solve the inverse problem, to find a sequence that matches a protein backbone. 20 Mar 2025 | stringtie updated to version 3.0.1 | StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. It is primarily a genome-guided transcriptome assembler, although it can borrow algorithmic techniques from de novo genome assembly to help with transcript assembly. 19 Mar 2025 | CABSdock updated to version 0.9.18 | CABSdock is a standalone application for molecular docking of peptides to proteins. The CABSdock allows for flexible docking (also with large-scale conformational changes) without knowledge about the binding site. The CABSdock enables peptide docking using only information about the peptide sequence and the protein receptor structure. 14 Mar 2025 | DeepTMHMM updated to version 1.0 | A deep learning model for transmembrane topology prediction and classification 14 Mar 2025 | masurca updated to version 4.1.2 | Maryland Super Read Cabog Assembler genome assembly and analysis toolkit. Includes QuORUM error corrector for Illumina data, POLCA genome polishing software, and Chromosome scaffolder. 13 Mar 2025 | smrtanalysis updated to version 25.2 | 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. 13 Mar 2025 | gubbins updated to version 3.4 | 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. 13 Mar 2025 | BindCraft updated to version 1.5.0 | BindCraft is an open-source and automated pipeline for de novo protein binder design pipeline using AlphaFold2 backpropagation, MPNN, and PyRosetta. 13 Mar 2025 | Freesurfer updated to version 8.0.0 | 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. 12 Mar 2025 | PEPATAC updated to version 0.12.2 | PEPATAC is a robust pipeline for Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) built on a loosely coupled modular framework. It may be easily applied to ATAC-seq projects of any size, from one-off experiments to large-scale sequencing projects. It is optimized on unique features of ATAC-seq data to be fast and accurate and provides several unique analytical approaches. 10 Mar 2025 | R updated to version 4.4.3 | R (the R Project) is a language and environment for statistical computing and graphics. R is similar to S, and provides a wide variety of statistical and graphical techniques (linear and nonlinear modelling, statistical tests, time series analysis, classification, clustering, ...). 7 Mar 2025 | deepict updated to version 1.0.0 | DeePiCt (Deep Picker in Context), a deep-learning based pipeline to achieve structure segmentation and particle localization in cryo-electron tomography. DeePiCt combines two dedicated convolutional networks: a 2D CNN for segmentation of cellular compartments (e.g. organelles or cytosol), and a 3D CNN for particle localization and structure segmentation. 6 Mar 2025 | VEP updated to version 113 | VEP (Variant Effect Predictor) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. 6 Mar 2025 | deeptools updated to version 3.5.6 | deepTools is a suite of user-friendly tools for the visualization, quality control and normalization of data from deep-sequencing DNA sequencing experiments. 6 Mar 2025 | csvkit updated to version 2.1.0 | csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. 5 Mar 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. 5 Mar 2025 | diann updated to version 2.0.2 | DIA-NN - a universal software for data-independent acquisition (DIA) proteomics data processing 3 Mar 2025 | rdfind updated to version 1.7.0 | rdfind is a program that finds duplicate files. It is useful for compressing backup directories or just finding duplicate files. It compares files based on their content, NOT on their file names. After typing module load rdfind, type man rdfind for more information. 3 Mar 2025 | sodium updated to version 1.0.20 | Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing, and more. 3 Mar 2025 | SciTE updated to version 5.5.5 | 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. 3 Mar 2025 | EDirect updated to version 23.5.20250228 | Entrez Direct (EDirect) is an advanced method for accessing the NCBI's set of interconnected databases (publication, sequence, structure, gene, variation, expression, etc.) from a UNIX terminal window. 28 Feb 2025 | spaceranger updated to version 3.1.3 | 10x pipeline for processing Visium spatial RNA-seq data 28 Feb 2025 | cellranger updated to version 9.0.1 | 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. 27 Feb 2025 | sirvsuite updated to version 0.1.3 | QC tool for RNA-Seq workflow using Lexogen's SIRV spike-in controls 25 Feb 2025 | alphafold3 updated to version 3.0.1 | This package provides an implementation of the inference pipeline of AlphaFold 3 25 Feb 2025 | uv updated to version 0.6.3 | An extremely fast Python package and project manager, written in Rust. 24 Feb 2025 | zstd updated to version 1.5.7 | Zstandard, or zstd as short version, is a fast lossless compression algorithm, targeting real-time compression scenarios at zlib-level and better compression ratios. 21 Feb 2025 | hyperqueue updated to version 0.21.1 | HyperQueue (HQ) lets you build a computation plan consisting of a large amount of tasks and then execute it transparently over a system like SLURM/PBS. It dynamically groups tasks into SLURM/PBS jobs and distributes them to fully utilize allocated nodes. 20 Feb 2025 | bwulf updated to version 0.3.1 | unified interface to custom utilities by the NIH HPC staff. 19 Feb 2025 | gromacs updated to version 2024.4 | Gromacs is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. It is primarily designed for biochemical molecules like proteins and lipids that have a lot of complicated bonded interactions, but since GROMACS is extremely fast at calculating the nonbonded interactions (that usually dominate simulations) many groups are also using it for research on non-biological systems, e.g. polymers. 14 Feb 2025 | vg updated to version 1.63.1 | Tools for working with genome variation graphs 13 Feb 2025 | MUMmer updated to version 4.0.1 | Mummer is a system for aligning entire genomes extremely rapidly. 13 Feb 2025 | fraposa updated to version 032123 | Fraposa predicts the ancestry of study samples by using principle component analysis (PCA) with a reference panel. 10 Feb 2025 | hitips updated to version 1.0.12 | HiTIPS: High-Throughput Image Processing Software for the Study of Nuclear Architecture and Gene Expression. Documentations: https://hitips.readthedocs.io/en/latest/ 10 Feb 2025 | esm updated to version 3.1.2 | Code and pre-trained weights for Transformer protein language models from the Meta Fundamental AI Research Protein Team (FAIR) 5 Feb 2025 | marp updated to version 4.1.1 | A CLI for Marp and any slide deck converter based on Marpit framework. It can convert Marp / Marpit Markdown files into static HTML / CSS, PDF, PowerPoint document, and image(s) easily. 4 Feb 2025 | nodejs updated to version 22.13.1 | Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs 4 Feb 2025 | longshot updated to version 1.0.0 | Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs). 31 Jan 2025 | modkit updated to version 0.4.3 | 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. 29 Jan 2025 | ccpem updated to version 1.6.0 | The Collaborative Computational Project for electron cryo-microscopy (CCP-EM) supports users and developers in biological cryogenic EM. 27 Jan 2025 | famdb updated to version 1.0.5 | 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. 27 Jan 2025 | PyRosetta updated to version 387.py3.12 | PyRosetta is an interactive Python-based interface to the powerful Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions. 27 Jan 2025 | pixi updated to version 0.40.3 | pixi is a cross-platform, multi-language package manager and workflow tool built on the foundation of the conda ecosystem. It provides developers with an exceptional experience similar to popular package managers like cargo or yarn, but for any language. 23 Jan 2025 | OmicCircosShiny updated to version 250121 | Shiny wrapper for R OmicCircos package. Only used in OpenOndemand 22 Jan 2025 | Genome Browser updated to version 476 | 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. |
For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data