NCBI - National Center for Biotechnology Information/NLM/NIH

sra-tools

SRA Tools

datasets

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

pgap

NCBI Prokaryotic Genome Annotation Pipeline

amr

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

icn3d

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

egapx

Eukaryotic Genome Annotation Pipeline-External caller scripts and documentation

vadr

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

ngs-tools

ncbi-vdb

ncbi-vdb

SSDraw

clinvar

ClinVar aggregates information about genomic variation and its relationship to human health. Contact us at 'clinvar@ncbi.nlm.nih.gov' with any questions or comments.

ncbi-cxx-toolkit-public

NCBI C++ Toolkit package sources

elastic-blast

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

docker

sra-human-scrubber

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.

tree-tool

Incremental building of phylogenetic distance trees

EvoGeneX

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.

fcs-gx

Foreign Contamination Screening - GX source code

cwl-ngs-workflows-cbb

A set of CWL tools and workflows used by NCBI Computational Biology Branch for NGS data analysis

cxx-toolkit

stxtyper

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

pubchem-align3d

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.

ncbi-cxx-toolkit-conan

NCBI C++ Toolkit package recipe

CF-random_software

Prediction of alternative conformation and fold-switching proteins with ColabFold

elastic-blast-docs

ElasticBLAST documentation

ncbi-logging

Log monitoring and gathering infrastructure to feed analytics

International-Protein-Nomenclature-Guidelines

International Protein Nomenclature Guidelines

ncbi-vdb-conan

Conan package recipe for NCBI VDB Toolkit

rnaseq_gene_counts

RNAseq gene counts

workshop-sra-hands-on

SRA Outreach to the NIH Research Festival and ASHG 2025