NCncats
Virus

Get a virus genome data package by taxon

Changed on

Download a virus genome data package including sequence, annotation, BioSample data and a detailed data report by taxon.

get/virus/taxon/{taxon}/genome/download

Request

  • Base URL
    https://api.ncbi.nlm.nih.gov/datasets/v2
  • Auth
    API key in header api-key

Path parameters

taxonstring required

NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank

Query parameters

refseq_onlyboolean

If true, limit results to RefSeq genomes.

annotated_onlyboolean

If true, limit results to annotated genomes.

released_sincestring date-time
updated_sincestring date-time
hoststring

Limit to genomes isolated from the specified host species (NCBI Taxonomy ID, common or scientific name).

pangolin_classificationstring

Limit to SARS-CoV-2 genomes from the specified Pango lineage.

geo_locationstring

Limit to genomes collected from the specified geographic location.

usa_statestring

Limit to genomes collected from the specified U.S. state (two-letter abbreviation).

complete_onlyboolean

Limit to genomes designated as complete, as defined by the submitter.

include_sequenceV2ViralSequenceType[]

Specify which sequence files to include in the data package.

aux_reportV2VirusDatasetReportType[]

Specify which report files to include in the data package. The virus data report is always included, and its inclusion is not affected by this parameter.

use_psgboolean

Experimental approach to retrieving sequence data.

filenamestring

Output file name.

Response

A successful response

Changes

  • e5d4400c8e5dRevision changes
    • breaking

      removed the enum value BIOSAMPLE from the property items/ of the query request parameter include_sequence

    • warning

      deleted the query request parameter taxons

  • 00bdccfc6283Revision changes
    • breaking

      removed the media type application/json for the response with the status

    • info

      added the new optional query request parameter taxons

    • info

      added the new optional query request parameter usa_state

    • info

      added the media type text/plain for the response with the status