Application updates in the last 3 months
To see all versions available for any application, use module avail application_name
All centrally-installed applications are listed on the Applications page
Updated Application
4 Aug 2026 rfd3 updated to version 0.2.0
RFD3 (RFdiffusion3) uses an atom-level diffusion framework to design proteins around ligands, nucleic acids, and other nonprotein molecular components. Because it generates complete atomic structures rather than only protein backbones, it can incorporate detailed geometric constraints for applications such as enzyme engineering and the design of proteins that bind small molecules or DNA.
3 Aug 2026 dorado updated to version 2.1.1
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads.
28 Jul 2026 NAMD updated to version 3.0.2
NAMD is a parallel molecular dynamics program for UNIX platforms designed for high-performance simulations in structural biology. VMD, the associated molecular visualization program, is also available.
27 Jul 2026 LAST updated to version 1652
LAST is designed for moderately large data (e.g. genomes, DNA reads, proteomes). It's especially geared toward:
  • Finding rearrangements and recombinations (last-split)
  • Finding DNA-versus-protein related regions, especially protein fossils.
  • Unusual data, e.g. AT-rich DNA, because it can fit parameters to the data and calculate significance.
  • Sensitive DNA-DNA search, due to fitting, sensitive seeding, and calculating significance.
27 Jul 2026 Genome Browser updated to version 501
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.
24 Jul 2026 sqanti3 updated to version 6.0.2
Quality control of long-read transcriptomes.
24 Jul 2026 jvarkit updated to version 20260430
Java tools for bioinformatics
23 Jul 2026 eggNOG-mapper updated to version 2.1.15
eggNOGmapper is a tool for functional annotation of large sets of sequences based on fast orthology assignments using precomputed clusters and phylogenies from the eggNOG database. Orthology assignment is ideally suited for functional inference. However, predicting orthology is computationally intensive at large scale, and most other pipelines are relatively inaccessible (e.g., new assignments only available through database updates), so less precise homology-based functional transfer was previously the default for (meta-)genome annotation.
23 Jul 2026 tomoDRGN updated to version v1.0.4
TomoDRGN extends the cryoDRGN framework to cryo-ET by learning heterogeneity from datasets in which each particle is sampled by multiple projection images at different stage tilt angles. For cryo-ET samples imaging particles in situ, tomoDRGN therefore enables continuous heterogeneity analysis at a single particle level within the native cellular environment.
23 Jul 2026 petprep updated to version 0.0.8
Pre-processing of PET datasets: Motion correction, segment anatomy, registration, volume correction, generation of quality reports, and others using tools from several neuroimaging applications such as FSL, ANTs, freesurfer, AFNI.
22 Jul 2026 Clair3 updated to version 2.0.2
Clair3 is a small variant caller for Illumina, PacBio and ONT long reads. Compare to PEPPER (r0.4), Clair3 (v0.1) shows a better SNP F1-score with ≤30-fold of ONT data (precisionFDA Truth Challenge V2), and a better Indel F1-score, while runs generally four times faster.
22 Jul 2026 parallel updated to version 20260722
GNU parallel is a shell tool for executing jobs in parallel using one or more computers.
22 Jul 2026 Meryl updated to version 1.4.2
Meryl: a genomic k-mer counter (and sequence utility) with nice features. It is built into the Celera Assembler and is also available as a stand-alone application. Meryl uses a sorting-based approach that sorts the k-mers in lexicographical order.
22 Jul 2026 ollama updated to version 0.32.2
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.
21 Jul 2026 whatshap updated to version 2.8
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.
21 Jul 2026 augustus updated to version 3.5.0
AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences.
21 Jul 2026 rmblast updated to version 2.17.1
RMBlast is a RepeatMasker-compatible version of the standard NCBI blastn program. RMBlast supports RepeatMasker searches by adding a few necessary features to the stock NCBI blastn program.
21 Jul 2026 preseq updated to version 3.2.0
predicting library complexity and genome coverage in high-throughput sequencing
20 Jul 2026 RepeatMasker updated to version 4.2.4
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.
17 Jul 2026 merqury updated to version 1.4.1
Evaluate genome assemblies with k-mers and more
16 Jul 2026 baysor updated to version 0.8.2
15 Jul 2026 mbg updated to version 1.0.17
Minimizer based sparse de Bruijn Graph constructor.
15 Jul 2026 kallisto updated to version 0.52.0
kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for rapidly determining the compatibility of reads with targets, without the need for alignment.
15 Jul 2026 plink updated to version 7.1-alpha
PLINK is whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.
15 Jul 2026 spades updated to version 4.3.0
SPAdes – St. Petersburg genome assembler – is intended for both standard isolates and single-cell MDA bacteria assemblies.
15 Jul 2026 PAML updated to version 4.10.10
A package of programs for phylogenetic analyses of DNA and protein sequences using maximum likelihood.
10 Jul 2026 sicer updated to version 2.1.1
A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
7 Jul 2026 cellranger updated to version 10.1.0
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.
6 Jul 2026 Perl updated to version 5.42
Perl is a highly capable, feature-rich programming language with over 30 years of development.
2 Jul 2026 boost updated to version 1.91
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.
30 Jun 2026 abyss updated to version 2.3.10
Abyss represents Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler. The parallel version is implemented using MPI and is capable of assembling larger genomes.
30 Jun 2026 csvkit updated to version 2.2.0
csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats.
29 Jun 2026 clark updated to version 1.4.5.0-a
A method based on a supervised sequence classification using discriminative k-mers
29 Jun 2026 circos updated to version 0.69-10
Circos is a program for the generation of publication-quality, circularly composited renditions of genomic data and related annotations. Circos is particularly suited for visualizing alignments, conservation and intra and inter-chromosomal relationships. Also, Circos is useful to visualize any type of information that benefits from a circular layout. Thus, although it has been designed for the field of genomics, it is sufficiently flexible to be used in other data domains.
29 Jun 2026 agat updated to version 1.7.0
Another Gtf/Gff Analysis Toolkit
29 Jun 2026 cnvkit updated to version 0.9.13
Copy number variant detection from targeted DNA sequencing
29 Jun 2026 rust updated to version 1.96.0
A language empowering everyone to build reliable and efficient software.
26 Jun 2026 salmon updated to version 2.1.2
a tool for quantifying the expression of transcripts using RNA-seq data.
26 Jun 2026 trimgalore updated to version 2.2.0
Consistent quality and adapter trimming for RRBS or standard FastQ files.
25 Jun 2026 PartekFlow updated to version 12.11.1
Web interface designed specifically for the analysis needs of next generation sequencing applications including RNA, small RNA, and DNA sequencing.
24 Jun 2026 htseq updated to version 2.1.2
HTSeq is a Python package that provides infrastructure to process data from high-throughput sequencing assays.
24 Jun 2026 bowtie2 updated to version 2.5.5
A version of bowtie that's particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes
23 Jun 2026 RevBayes updated to version 1.4.0
Bayesian phylogenetic inference using probabilistic graphical models and an interpreted language
22 Jun 2026 vcfanno updated to version 0.3.9
annotate a VCF with other VCFs/BEDs/tabixed files
22 Jun 2026 nodejs updated to version 24.17.0
Node.js is a JavaScript runtime built on Chrome's V8 JavaScript engine. module name: nodejs
15 Jun 2026 famdb updated to version 3.0.0
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.
15 Jun 2026 kneaddata updated to version 0.12.4
KneadData is a tool designed to perform quality control on metagenomic and metatranscriptomic sequencing data, especially data from microbiome experiments.
15 Jun 2026 diamond updated to version 2.2.1
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.
11 Jun 2026 smrtanalysis updated to version 26.1
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.
11 Jun 2026 bamtofastq updated to version 1.4.1
Tool for converting 10x BAMs produced by Cell Ranger, Space Ranger, Cell Ranger ATAC, Cell Ranger DNA, and Long Ranger back to FASTQ files that can be used as inputs to re-run analysis.
11 Jun 2026 deepsomatic updated to version 1.10.0
DeepSomatic is a google developed analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal sequencing data.
11 Jun 2026 TRsv updated to version 1.1.2
Detection and Genotyping of Tandem Repeat Expansion/Contraction, Structural Variants (SVs), and Indels using Long Reads
11 Jun 2026 MultAlin updated to version 5.4.1
MultAlin creates a multiple sequence alignment from a group of related sequences using progressive pairwise alignments.
10 Jun 2026 yass updated to version 1.16_alpha1
yass is a genomic similarity seach tool for nucleic (and only nucleic) sequences in (multi)fasta or plain text format. yass produces local pairwise alignments in yass format, blast tabular format, or PSL format.
10 Jun 2026 SvABA updated to version 2.0.20260514
SvABA (formerly Snowman) is an SV and indel caller for short-read BAMs
10 Jun 2026 sniffles updated to version 2.8.0
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.
10 Jun 2026 gnomix updated to version 0-20260605
G-Nomix does high resolution ancestry deconvolution for high-throughput sequencing data.
10 Jun 2026 minimap2 updated to version 2.31
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).
9 Jun 2026 exomiser updated to version 15.1.0
The Exomiser is a Java program that functionally annotates variants from whole-exome sequencing data starting from a VCF file.
8 Jun 2026 novocraft updated to version 4.04.04
Package includes aligner for single-ended and paired-end reads from the Illumina Genome Analyser. Novoalign finds global optimum alignments using full Needleman-Wunsch algorithm with affine gap penalties.
8 Jun 2026 hyperqueue updated to version 0.26.2
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.
5 Jun 2026 aslprep updated to version 26.0.3
Aslprep is an application for preprocessing of ASL (arterial spin labeling) data and computation of CBF (cerebral blood flow). Aslprep is a pipeline that uses AFNI, FSL, ANTs, and freesurfer.
3 Jun 2026 alphafold3 updated to version 3.0.2
This package provides an implementation of the inference pipeline of AlphaFold 3
27 May 2026 freebayes updated to version 1.3.10
Bayesian haplotype-based polymorphism discovery and genotyping
22 May 2026 SimNIBS updated to version 4.6.0
SimNIBS is a free software package for the Simulation of Non-invasive Brain Stimulation. It allows for realistic calculations of the electric field induced by transcranial magnetic stimulation (TMS) and transcranial direct current stimulation (tDCS).
22 May 2026 stringtie updated to version 3.0.3
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.
21 May 2026 sratoolkit updated to version 3.4.0
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
21 May 2026 impute5 updated to version 1.2.0
IMPUTE 5 is a genotype imputation method that can scale to reference panels with millions of samples.
20 May 2026 isoquant updated to version 3.13.0
IsoQuant is used to analyze long read RNA sequencing data
19 May 2026 scanpy updated to version 1.12.1
Scanpy is a scalable toolkit for analyzing single-cell gene expression data. It includes preprocessing, visualization, clustering, pseudotime and trajectory inference and differential expression testing. The Python-based implementation efficiently deals with datasets of more than one million cells.
18 May 2026 apptainer updated to version 1.4.5
Apptainer allows you to build and run Linux containers with emphasis on use in HPC. Apptainer is the Linux Foundation variant of Singularity.
15 May 2026 modkit updated to version 0.6.2
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.
11 May 2026 raxml-ng updated to version 2.0.1
RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree. Successor to raxml.
7 May 2026 clair3-rna updated to version 0.2.2
Clair3-RNA is a small variant caller for long-read RNA sequencing (lrRNA-seq) data. Clair3-RNA supports ONT R10.4.1 and R9.4.1 complementary DNA sequencing (cDNA) and direct RNA sequencing (dRNA). Clair3-RNA also supports PacBio Sequel and PacBio MAS-Seq RNA sequencing data.
7 May 2026 dragen_reports updated to version 4.4.4
6 May 2026 PGAP updated to version 2026-04-27.build8516
The NCBI Prokaryotic Genome Annotation Pipeline (PGAP) is designed to annotate bacterial and archaeal genomes (chromosomes and plasmids).
Scientific Databases updated in last 3 months

For a full list of scientific databases available and updated on the NIH HPC systems, see HPC Reference Data