taxon
Print a data report containing virus genome metadata by taxon (NCBI Taxonomy ID, scientific or common name for any virus at any tax rank)
taxon
Name
datasets summary virus genome taxon - Print a data report containing virus genome metadata by taxon (NCBI Taxonomy ID, scientific or common name for any virus at any tax rank)
Synopsis
datasets summary virus genome taxon [flags]
Description
Print a data report containing virus genome metadata by taxon (NCBI Taxonomy ID, scientific or common name for any virus at any tax rank). The data report is returned in JSON format
Refer to NCBI’s download and install documentation for information about getting started with the command-line tools.
Examples
datasets summary virus genome taxon sars-cov-2 --host dog
Options
--annotated Limit to annotated genomes
--api-key string Specify an NCBI API key
--as-json-lines Output results in JSON Lines format
--complete-only Limit to complete genomes
--debug Emit debugging info
--geo-location string Limit to genomes isolated from a specified geographic location (continent or country)
--help Print detailed help about a datasets command
--host string Limit to virus genomes isolated from a specified host species
--inputfile string Read a list of NCBI taxonomy identifiers (taxid or current scientific name) from a file to use as input (max: 100)
--limit string Limit the number of virus summaries returned
* all: returns all matching virus summaries
* a number: returns the specified number of matching virus summaries
(default "all")
--lineage string Limit results by Pango lineage (only SARS-CoV-2)
--refseq Limit to RefSeq genomes
--released-after string Limit to genomes released on or after a specified date (free format, ISO 8601 YYYY-MM-DD recommended)
--report string Specify report virus genome report summary type
* virus: returns a primary virus data report
* annotation: returns a virus annotation report
(default "virus")
--updated-after string Limit to genomes updated on or after a specified date (free format, ISO 8601 YYYY-MM-DD recommended)
--usa-state string Limit to genomes isolated from a specified U.S. state (two-letter abbreviation)
--version Print version of datasets
Generated February 26, 2025