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    161 repositories

    • ncbi-cxx-toolkit-public

      Public
      NCBI C++ Toolkit package sources
      C++
      •
      Other
      •35•75•0•0•Updated Aug 10, 2025Aug 10, 2025

    • sra-tools

      Public
      SRA Tools
      C
      •
      Other
      •266•1.2k•23•6•Updated Aug 8, 2025Aug 8, 2025

    • tree-tool

      Public
      Incremental building of phylogenetic distance trees
      bioinformaticsevolutionphylogenetic-treesdata-analysisdistance-measuresbioinformatics-tool
      HTML
      •
      Other
      •10•25•0•1•Updated Aug 8, 2025Aug 8, 2025

    • ncbi-vdb

      Public
      ncbi-vdb
      C
      •
      Other
      •42•92•10•2•Updated Aug 7, 2025Aug 7, 2025

    • cwl-ngs-workflows-cbb

      Public
      A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis
      ngsngs-analysisngs-pipelinecwl-workflow
      Common Workflow Language
      •
      Other
      •10•24•0•0•Updated Aug 7, 2025Aug 7, 2025

    • ncbi-cxx-toolkit-conan

      Public
      NCBI C++ Toolkit package recipe
      Python
      •10•10•0•0•Updated Aug 5, 2025Aug 5, 2025

    • datasets

      Public
      NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
      ncbigenomics-data
      Jupyter Notebook
      •
      Other
      •52•444•20•2•Updated Aug 1, 2025Aug 1, 2025

    • cxx-toolkit

      Public
      HTML
      •
      The Unlicense
      •51•21•0•0•Updated Jul 31, 2025Jul 31, 2025

    • clinvar

      Public
      ClinVar aggregates information about genomic variation and its relationship to human health. Contact us at '[email protected]' with any questions or comments.
      HTML
      •17•81•4•0•Updated Jul 30, 2025Jul 30, 2025

    • docker

      Public
      Dockerfile
      •
      Other
      •34•54•2•0•Updated Jul 30, 2025Jul 30, 2025

    • ncbi-logging

      Public
      Log monitoring and gathering infrastructure to feed analytics
      C++
      •9•7•0•2•Updated Jul 30, 2025Jul 30, 2025

    • icn3d

      Public
      web-based protein structure viewer and analysis tool interactively or in batch mode
      nodejsdelphiwebglvrarjupyter-notebookchemicalproteinsnpnucleotide
      JavaScript
      •
      Other
      •49•168•7•2•Updated Jul 28, 2025Jul 28, 2025

    • rnaseq_gene_counts

      Public
      RNAseq gene counts
      0•0•0•0•Updated Jul 25, 2025Jul 25, 2025

    • sra-human-scrubber

      Public
      An SRA tool that takes as input local fastq file from a clinical infection sample, identifies and removes any significant human read, and outputs the edited (cleaned) fastq file that can safely be used for SRA submission.
      Shell
      •
      Other
      •10•50•3•0•Updated Jul 24, 2025Jul 24, 2025

    • pgap

      Public
      NCBI Prokaryotic Genome Annotation Pipeline
      Common Workflow Language
      •
      Other
      •96•348•2•0•Updated Jul 23, 2025Jul 23, 2025

    • amr

      Public
      AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
      genomicspathogenantibiotic-resistancebioinformatics
      C++
      •
      Other
      •46•319•10•0•Updated Jul 22, 2025Jul 22, 2025

    • stxtyper

      Public
      StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
      bioinformaticsgenomicspathogenescherichia-colibioinformatics-toolvirulence-genes
      C++
      •
      Other
      •7•17•1•0•Updated Jul 16, 2025Jul 16, 2025

    • egapx

      Public
      Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
      Nextflow
      •
      Other
      •16•147•19•0•Updated Jul 15, 2025Jul 15, 2025

    • elastic-blast-docs

      Public
      ElasticBLAST documentation
      Other
      •5•8•0•0•Updated Jul 15, 2025Jul 15, 2025

    • vadr

      Public
      Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
      Perl
      •
      Other
      •27•110•7•0•Updated Jun 20, 2025Jun 20, 2025

    • ngs-tools

      Public
      C++
      •
      Other
      •25•107•8•4•Updated Jun 18, 2025Jun 18, 2025

    • CF-random_software

      Public
      Prediction of alternative conformation and fold-switching proteins with ColabFold
      Python
      •
      Other
      •1•6•0•0•Updated Jun 10, 2025Jun 10, 2025

    • fcs-gx

      Public
      Foreign Contamination Screening - GX source code
      C++
      •
      Other
      •5•23•9•0•Updated Jun 9, 2025Jun 9, 2025

    • EvoGeneX

      Public
      This repository contains the source code of the R package for EvoGeneX, a software to infer the mode of evolution from the gene expression data.
      HTML
      •
      GNU General Public License v3.0
      •6•23•2•0•Updated Jun 2, 2025Jun 2, 2025

    • elastic-blast

      Public
      ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
      bioinformaticsblastncbi
      Python
      •
      Other
      •18•63•3•0•Updated May 21, 2025May 21, 2025

    • BioREx

      Public
      Python
      •10•37•2•0•Updated May 17, 2025May 17, 2025

    • GeneGPT

      Public
      Code and data for GeneGPT.
      Python
      •
      Other
      •35•409•0•0•Updated May 8, 2025May 8, 2025

    • igblast

      Public
      CSS
      •9•6•0•0•Updated Apr 18, 2025Apr 18, 2025

    • magicblast

      Public
      Python
      •15•37•13•0•Updated Apr 17, 2025Apr 17, 2025

    • rapt

      Public archive
      This RAPT repository has been retired as of December 2024. NCBI's Read assembly and Annotation Pipeline Tool (RAPT) was a pilot service.
      ngsgenome-annotationpgapannotation-pipelineskesa
      17•58•0•0•Updated Apr 1, 2025Apr 1, 2025