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    162 repositories

    • sra-tools

      Public
      SRA Tools
      C
      •
      Other
      •270•1.3k•22•5•Updated Oct 22, 2025Oct 22, 2025

    • ncbi-cxx-toolkit-public

      Public
      NCBI C++ Toolkit package sources
      C++
      •
      Other
      •37•78•1•0•Updated Oct 22, 2025Oct 22, 2025

    • tree-tool

      Public
      Incremental building of phylogenetic distance trees
      bioinformaticsevolutionphylogenetic-treesdata-analysisdistance-measuresbioinformatics-tool
      HTML
      •
      Other
      •10•26•0•1•Updated Oct 21, 2025Oct 21, 2025

    • ngs-tools

      Public
      C++
      •
      Other
      •25•107•8•4•Updated Oct 20, 2025Oct 20, 2025

    • ncbi-vdb

      Public
      ncbi-vdb
      C
      •
      Other
      •42•91•10•2•Updated Oct 20, 2025Oct 20, 2025

    • pgap

      Public
      NCBI Prokaryotic Genome Annotation Pipeline
      Common Workflow Language
      •
      Other
      •95•355•0•0•Updated Oct 16, 2025Oct 16, 2025

    • cxx-toolkit

      Public
      HTML
      •
      The Unlicense
      •52•19•0•0•Updated Oct 15, 2025Oct 15, 2025

    • ncbi-cxx-toolkit-conan

      Public
      NCBI C++ Toolkit package recipe
      Python
      •10•9•0•0•Updated Oct 6, 2025Oct 6, 2025

    • vadr

      Public
      Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
      Perl
      •
      Other
      •27•109•8•0•Updated Oct 1, 2025Oct 1, 2025

    • datasets

      Public
      NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
      ncbigenomics-data
      Jupyter Notebook
      •
      Other
      •56•472•22•1•Updated Sep 30, 2025Sep 30, 2025

    • amr

      Public
      AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
      bioinformaticsgenomicspathogenantibiotic-resistance
      C++
      •
      Other
      •47•327•11•0•Updated Sep 26, 2025Sep 26, 2025

    • pm4ngs

      Public
      Project Manager for NGS data analysis
      bioinformaticsnext-generation-sequencingrnaseqngs-analysisngs-pipelinecwl-workflowchipseqchipexo
      Python
      •
      Other
      •10•30•0•0•Updated Sep 25, 2025Sep 25, 2025

    • icn3d

      Public
      web-based protein structure viewer and analysis tool interactively or in batch mode
      nodejsdelphiwebglvrarjupyter-notebookchemicalproteinsnpnucleotide
      JavaScript
      •
      Other
      •50•168•7•2•Updated Sep 22, 2025Sep 22, 2025

    • ncbi-logging

      Public
      Log monitoring and gathering infrastructure to feed analytics
      C++
      •9•9•0•2•Updated Sep 19, 2025Sep 19, 2025

    • ncbi-vdb-conan

      Public
      Conan package recipe for NCBI VDB Toolkit
      Python
      •1•0•0•0•Updated Sep 12, 2025Sep 12, 2025

    • workshop-sra-hands-on

      Public
      SRA Outreach to the NIH Research Festival and ASHG 2025
      0•0•0•0•Updated Sep 10, 2025Sep 10, 2025

    • SSDraw

      Public
      Jupyter Notebook
      •
      Other
      •11•84•2•0•Updated Sep 3, 2025Sep 3, 2025

    • pubchem-align3d

      Public
      This is a generic C++ library that can be used to rapidly align two small molecules in 3D space, with shape - and optionally color - Tanimoto scoring. Included is a sample RDKit application whereby any two SDF-format chemicals are read in and aligned.
      C++
      •
      Other
      •4•14•1•0•Updated Sep 3, 2025Sep 3, 2025

    • International-Protein-Nomenclature-Guidelines

      Public
      International Protein Nomenclature Guidelines
      7•1•0•0•Updated Aug 20, 2025Aug 20, 2025

    • CF-random_software

      Public
      Prediction of alternative conformation and fold-switching proteins with ColabFold
      Python
      •
      Other
      •1•8•0•0•Updated Aug 19, 2025Aug 19, 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

    • 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•53•2•0•Updated Jul 30, 2025Jul 30, 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•48•3•0•Updated Jul 24, 2025Jul 24, 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•164•36•0•Updated Jul 15, 2025Jul 15, 2025

    • elastic-blast-docs

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

    • fcs-gx

      Public
      Foreign Contamination Screening - GX source code
      C++
      •
      Other
      •5•24•12•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•26•2•0•Updated Jun 2, 2025Jun 2, 2025