taxon

Name

datasets summary genome taxon - print a summary of a genome dataset by taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)

Synopsis

datasets summary genome taxon [flags]

Description

Print a summary of a genome dataset by taxon (NCBI Taxonomy ID, scientific or common name at any tax rank). The summary 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 genome taxon human
  datasets summary genome taxon "mus musculus"
  datasets summary genome taxon 10116

Options

  -a, --annotated                only include genomes with annotation
      --api-key string           NCBI Datasets API Key
      --as-json-lines            Stream results as newline delimited JSON-Lines
      --assembly-level string    restrict assemblies to a comma-separated list of one or more of: chromosome, complete_genome, contig, scaffold
      --assembly-source string   restrict assemblies to refseq or genbank only
      --assmaccs                 return only assembly accessions
  -h, --help                     help for taxon
      --limit string             limit the number of genome summaries returned
                                 * "all": returns all matching genome summaries
                                 * "none": returns only the number of matching genome summaries
                                 * a number: returns the specified number of matching genome summaries
                                  (default "all")
      --no-progressbar           hide progress bar
      --reference                limit to reference and representative (GCF_ and GCA_) assemblies
      --released-before string   only include genomes that have been released before a specified date (MM/DD/YYYY)
      --released-since string    only include genomes that have been released after a specified date (MM/DD/YYYY)
      --search strings           only include genomes that have the specified text in the
                                 searchable fields: species and infraspecies, assembly name and submitter
                                 To provide multiple strings '--search' can be included multiple times
      --tax-exact-match          exclude sub-species when a species-level taxon is specified