taxon

Name

datasets summary virus genome taxon - Print coronavirus genome metadata by accession

Synopsis

datasets summary virus genome taxon [flags]

Description

Print coronavirus genome metadata (data report) by taxa in the Coronaviridae family. 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

  -a, --annotated               only include viral genomes with annotation
      --api-key string          NCBI Datasets API Key
      --as-json-lines           stream results as newline delimited JSON-Lines
      --complete-only           only include complete coronavirus data reports
      --geo-location string     limit to coronavirus genomes isolated from a specified geographic location (continent, country or U.S. state)
  -h, --help                    help for taxon
      --host string             limit to coronavirus genomes isolated from a specified host (NCBI Taxonomy ID, scientific or common name at any taxonomic rank)
      --limit string            limit the number of genome summaries returned
                                	* "all": returns all matching virus data reports
                                	* "none": returns only the number of matching virus data reports
                                	* a number: returns the specified number of matching data reports
                                	 (default "all")
      --lineage string          limit to SARS-CoV-2 genomes classified as the specified lineage (variant) by pangolin using the pangoLEARN algorithm
      --no-progressbar          hide progress bar
      --refseq                  limit to RefSeq coronavirus genomes
      --released-since string   limit to coronavirus genomes released after a specified date (MM/DD/YYYY)
      --updated-since string    limit to coronavirus genomes updated after a specified date (MM/DD/YYYY)