Repositories list

• ncbi-cxx-toolkit-public

  Public
  NCBI C++ Toolkit package sources

  C++

  •

  Other

  •28•63•1•0•Updated Mar 13, 2025Mar 13, 2025

• cxx-toolkit

  Public
  HTML

  •

  The Unlicense

  •47•20•0•0•Updated Mar 12, 2025Mar 12, 2025

• sra-tools

  Public
  SRA Tools

  C

  •

  Other

  •256•1.2k•85•9•Updated Mar 12, 2025Mar 12, 2025

• ncbi-vdb

  Public
  ncbi-vdb

  C

  •

  Other

  •40•91•11•3•Updated Mar 12, 2025Mar 12, 2025

• vadr

  Public
  Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation

  Perl

  •

  Other

  •27•108•7•0•Updated Mar 12, 2025Mar 12, 2025

• ncbi-logging

  Public
  Log monitoring and gathering infrastructure to feed analytics

  C++

  •8•6•0•1•Updated Mar 12, 2025Mar 12, 2025

• pgap

  Public
  NCBI Prokaryotic Genome Annotation Pipeline

  Common Workflow Language

  •

  Other

  •94•329•8•0•Updated Mar 12, 2025Mar 12, 2025

• datasets

  Public
  NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.

  ncbigenomics-data

  Jupyter Notebook

  •

  Other

  •46•391•23•0•Updated Mar 12, 2025Mar 12, 2025

• tree-tool

  Public
  Incremental building of phylogenetic distance trees

  bioinformaticsevolutionphylogenetic-trees+ 3data-analysisdistance-measuresbioinformatics-tool

  HTML

  •

  Other

  •8•22•0•1•Updated Mar 11, 2025Mar 11, 2025

• elastic-blast-docs

  Public
  ElasticBLAST documentation

  Other

  •5•5•0•0•Updated Mar 10, 2025Mar 10, 2025

• submission-schema

  Public
  0•1•0•0•Updated Mar 7, 2025Mar 7, 2025

• ncbi-cxx-toolkit-conan

  Public
  NCBI C++ Toolkit package recipe

  Python

  •8•9•0•0•Updated Mar 5, 2025Mar 5, 2025

• icn3d

  Public
  web-based protein structure viewer and analysis tool interactively or in batch mode

  nodejsdelphiwebgl+ 13vrarjupyter-notebookchemicalproteinsnpnucleotide+ 6

  JavaScript

  •

  Other

  •43•161•7•2•Updated Mar 3, 2025Mar 3, 2025

• fcs

  Public
  Foreign Contamination Screening caller scripts and documentation

  Other

  •16•127•14•0•Updated Mar 3, 2025Mar 3, 2025

• stxtyper

  Public
  StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.

  bioinformaticsgenomicspathogen+ 3escherichia-colibioinformatics-toolvirulence-genes

  C++

  •

  Other

  •5•13•1•1•Updated Feb 26, 2025Feb 26, 2025

• AF2_benchmark

  Public
  Jupyter Notebook

  •3•15•0•0•Updated Feb 25, 2025Feb 25, 2025

• amr

  Public
  AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.

  genomicspathogenantibiotic-resistance+ 1bioinformatics

  C++

  •

  Other

  •44•297•10•0•Updated Feb 21, 2025Feb 21, 2025

• BioREx

  Public
  Python

  •9•33•2•0•Updated Feb 7, 2025Feb 7, 2025

• ncbi-vdb-conan

  Public
  Conan package recipe for NCBI VDB Toolkit

  Python

  •1•1•0•0•Updated Jan 31, 2025Jan 31, 2025

• ngs-tools

  Public
  C++

  •

  Other

  •25•106•9•4•Updated Jan 15, 2025Jan 15, 2025

• elastic-blast

  Public
  ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective

  bioinformaticsblastncbi

  Python

  •

  Other

  •17•51•3•1•Updated Jan 13, 2025Jan 13, 2025

• DbGaP-FHIR-API-Docs

  Public
  The documentation repository for the dbGaP FHIR API.

  documentationfhirphenotypes

  Jupyter Notebook

  •

  Other

  •3•11•5•0•Updated Jan 7, 2025Jan 7, 2025

• egapx

  Public
  Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

  Nextflow

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  Other

  •13•117•6•0•Updated Jan 7, 2025Jan 7, 2025

• ribovore

  Public
  Perl

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  Other

  •5•16•3•0•Updated Dec 16, 2024Dec 16, 2024

• BAMscale

  Public
  BAMscale is a one-step tool for either 1) quantifying and normalizing the coverage of peaks or 2) generated scaled BigWig files for easy visualization of commonly used DNA-seq capture based methods.

  C

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  Other

  •17•68•1•1•Updated Dec 4, 2024Dec 4, 2024

• 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

  •16•77•4•0•Updated Nov 25, 2024Nov 25, 2024

• nongenomic-evolution-of-tumor-subclones

  Public
  Python

  •1•3•0•0•Updated Nov 5, 2024Nov 5, 2024

• SpaceProfiler

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Oct 30, 2024Oct 30, 2024

• SKESA

  Public
  SKESA assembler

  C++

  •

  Other

  •20•115•18•2•Updated Oct 11, 2024Oct 11, 2024

• workshop-asm-ngs-2024

  Public
  Pre-conference workshop for ASM NGS 2024

  1•7•0•0•Updated Oct 10, 2024Oct 10, 2024