NCBI - National Center for Biotechnology Information/NLM/NIH

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160 repositories

amr
Public
AMRFinderPlus - Identify AMR genes and point mutations, and virulence and stress resistance genes in assembled bacterial nucleotide and protein sequence.
genomics pathogen antibiotic-resistance bioinformatics
C++
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Other
•46•315•10•0•Updated Jun 21, 2025Jun 21, 2025
sra-tools
Public
SRA Tools
C
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Other
•259•1.2k•21•5•Updated Jun 20, 2025Jun 20, 2025
ncbi-vdb
Public
ncbi-vdb
C
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Other
•42•91•10•1•Updated Jun 20, 2025Jun 20, 2025
vadr
Public
Viral Annotation DefineR: classification and annotation of viral sequences based on RefSeq annotation
Perl
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Other
•27•110•7•0•Updated Jun 20, 2025Jun 20, 2025
ncbi-cxx-toolkit-public
Public
NCBI C++ Toolkit package sources
C++
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Other
•36•72•1•0•Updated Jun 20, 2025Jun 20, 2025
tree-tool
Public
Incremental building of phylogenetic distance trees
bioinformatics evolution phylogenetic-trees data-analysis distance-measures bioinformatics-tool
HTML
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Other
•10•25•0•1•Updated Jun 18, 2025Jun 18, 2025
ngs-tools
Public
C++
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Other
•25•107•8•4•Updated Jun 18, 2025Jun 18, 2025
ncbi-logging
Public
Log monitoring and gathering infrastructure to feed analytics
C++
•9•7•0•2•Updated Jun 17, 2025Jun 17, 2025
pgap
Public
NCBI Prokaryotic Genome Annotation Pipeline
Common Workflow Language
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Other
•94•339•1•0•Updated Jun 13, 2025Jun 13, 2025
icn3d
Public
web-based protein structure viewer and analysis tool interactively or in batch mode
nodejs delphi webgl vr ar jupyter-notebook chemical protein snp nucleotide
JavaScript
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Other
•47•166•7•2•Updated Jun 11, 2025Jun 11, 2025
CF-random_software
Public
Prediction of alternative conformation and fold-switching proteins with ColabFold
Python
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Other
•1•0•0•0•Updated Jun 10, 2025Jun 10, 2025
fcs-gx
Public
Foreign Contamination Screening - GX source code
C++
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Other
•4•21•8•0•Updated Jun 9, 2025Jun 9, 2025
cxx-toolkit
Public
HTML
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The Unlicense
•51•21•0•0•Updated Jun 6, 2025Jun 6, 2025
datasets
Public
NCBI Datasets is a new resource that lets you easily gather data from across NCBI databases.
ncbi genomics-data
Jupyter Notebook
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Other
•51•433•22•2•Updated Jun 5, 2025Jun 5, 2025
egapx
Public
Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation
Nextflow
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Other
•15•141•12•0•Updated Jun 5, 2025Jun 5, 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
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GNU General Public License v3.0
•6•21•2•0•Updated Jun 2, 2025Jun 2, 2025
ncbi-cxx-toolkit-conan
Public
NCBI C++ Toolkit package recipe
Python
•10•10•0•0•Updated May 29, 2025May 29, 2025
elastic-blast
Public
ElasticBLAST is a cloud-based tool to perform your BLAST searches faster and make you more effective
bioinformatics blast ncbi
Python
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Other
•18•60•3•0•Updated May 21, 2025May 21, 2025
BioREx
Public
Python
•9•36•2•0•Updated May 17, 2025May 17, 2025
stxtyper
Public
StxTyper uses a standardized algorithm to accurately type both known and unknown Shiga toxin operons from assembled genomic sequence.
bioinformatics genomics pathogen escherichia-coli bioinformatics-tool virulence-genes
C++
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Other
•7•16•1•0•Updated May 15, 2025May 15, 2025
GeneGPT
Public
Code and data for GeneGPT.
Python
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Other
•35•406•0•0•Updated May 8, 2025May 8, 2025
docker
Public
Dockerfile
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Other
•34•54•2•0•Updated Apr 22, 2025Apr 22, 2025
igblast
Public
CSS
•9•6•0•0•Updated Apr 18, 2025Apr 18, 2025
magicblast
Public
Python
•15•36•13•0•Updated Apr 17, 2025Apr 17, 2025
elastic-blast-docs
Public
ElasticBLAST documentation
Other
•5•8•0•0•Updated Apr 3, 2025Apr 3, 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.
ngs genome-annotation pgap annotation-pipeline skesa
17•57•0•0•Updated Apr 1, 2025Apr 1, 2025
DbGaP-FHIR-API-Docs
Public
The documentation repository for the dbGaP FHIR API.
documentation fhir phenotypes
Jupyter Notebook
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Other
•3•11•5•0•Updated Mar 31, 2025Mar 31, 2025
ribovore
Public
Perl
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Other
•5•16•3•0•Updated Mar 26, 2025Mar 26, 2025
ncbi-vdb-conan
Public
Conan package recipe for NCBI VDB Toolkit
Python
•1•1•0•0•Updated Mar 21, 2025Mar 21, 2025
submission-schema
Public
0•2•0•0•Updated Mar 18, 2025Mar 18, 2025