National Center for Biotechnology Information (NCBI)

National Center for Biotechnology Information (NCBI) Genome API

#### Options to download assembled genome data, including the associated sequence, annotation and metadata. These genome services allow you to get genome metadata as a data report or download genome, transcript and protein sequence, annotation and metadata as a genome data package, for assembled genomes.

GitHub OpenAPI

Operations 31

GET /genome/accession/{accessions}/download_summary Get a download summary (preview) of a genome data package by genome assembly… #
POST /genome/download_summary Get a download summary (preview) of a genome data package by genome assembly… #
GET /genome/accession/{accessions}/dataset_report Get a genome assembly report by genome assembly accession #
GET /genome/taxon/{taxons}/dataset_report Get a genome assembly report by taxon #
GET /genome/bioproject/{bioprojects}/dataset_report Get genome assembly reports by BioProject accession #
GET /genome/biosample/{biosample_ids}/dataset_report Get genome assembly reports by BioSample accession #
GET /genome/wgs/{wgs_accessions}/dataset_report Get a genome assembly data report by WGS accession #
GET /genome/assembly_name/{assembly_names}/dataset_report Get genome assembly reports by assembly name #
POST /genome/dataset_report Get a genome assembly report #
GET /genome/sequence_accession/{accession}/sequence_assemblies Get a genome assembly accession for a nucleotide sequence accession #
POST /genome/sequence_assemblies Get a genome assembly accession for a nucleotide sequence accession #
GET /genome/accession/{accession}/sequence_reports Get a genome sequence report by genome assembly accession #
POST /genome/sequence_reports Get a genome sequence report by genome assembly accession #
POST /genome/links Get assembly links by genome assembly accession #
GET /genome/taxon/{species_taxon}/checkm_histogram Get CheckM histogram data by species taxon #
POST /genome/checkm_histogram Get CheckM histogram data by species taxon #
GET /genome/accession/{accessions}/download Get a genome data package by genome assembly accession #
POST /genome/download Get a genome data package by genome assembly accession #
GET /genome/accession/{accession}/annotation_report/download Get a genome annotation data package by genome assembly accession #
POST /genome/annotation_report/download Get a genome annotation data package by genome assembly accession #
GET /genome/accession/{accessions}/check Check the validity of a genome assembly accession #
POST /genome/check Check the validity of a genome assembly accession #
GET /genome/accession/{accession}/annotation_report Get genome annotation reports by genome assembly accession #
POST /genome/annotation_report Get genome annotation reports by genome assembly accession #
GET /genome/accession/{accession}/annotation_summary Get genome annotation report summary information by genome assembly accession #
POST /genome/annotation_summary Get genome annotation report summary information by genome assembly accession #
GET /genome/accession/{accession}/annotation_report/download_summary Get a download summary (preview) of a genome annotation data package by genome… #
POST /genome/annotation_report/download_summary Get a download summary (preview) of a genome annotation data package by genome… #
GET /genome/accession/{accession}/revision_history Get a revision history for a genome assembly by genome assembly accession #
POST /genome/revision_history Get a revision history for a genome assembly by genome assembly accession #

Documentation

📖
Documentation
https://www.ncbi.nlm.nih.gov/datasets/docs/v2/api/rest-api/
📖
RateLimits
https://kinlane.github.io/ncbi/rate-limits/datasets.yml

Specifications

⚙
OpenAPI
https://raw.githubusercontent.com/api-evangelist/ncbi/refs/heads/main/openapi/ncbi-genome-api-openapi.yml

Other Resources

🔗
Plans
https://kinlane.github.io/ncbi/plans/datasets.yml

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OpenAPI Specification

ncbi-genome-api-openapi.yml Raw ↑ 
openapi: 3.2.0
info:
  title: NCBI Datasets Genome API
  version: v2
  description: '### NCBI Datasets is a resource that lets you easily gather data from NCBI.

    The NCBI Datasets version 2 API is updated often to add new features, fix bugs, and enhance usability.'
servers:
- url: https://api.ncbi.nlm.nih.gov/datasets/v2
security:
- ApiKeyAuthHeader: []
tags:


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# Full source: https://raw.githubusercontent.com/api-evangelist/ncbi/refs/heads/main/openapi/ncbi-genome-api-openapi.yml