taxon

Name

datasets summary genome taxon - Print a data report containing genome metadata by taxon (NCBI Taxonomy ID, scientific or common name at any tax rank)

Synopsis

datasets summary genome taxon [flags]

Description

Print a data report containing genome metadata by taxon (NCBI Taxonomy ID, scientific or common name at any tax rank). The data report is returned in JSON format.

Examples

  datasets summary genome taxon human
  datasets summary genome taxon "mus musculus"
  datasets summary genome taxon 10116

Options

      --annotated                 Limit to annotated genomes
      --api-key string            Specify an NCBI API key
      --as-json-lines             Output results in JSON Lines format
      --assembly-level string     Limit to genomes at one or more assembly levels (comma-separated):
                                    * chromosome
                                    * complete
                                    * contig
                                    * scaffold
                                     (default "[]")
      --assembly-source string    Limit to 'RefSeq' (GCF_) or 'GenBank' (GCA_) genomes (default "all")
      --assembly-version string   Limit to 'latest' assembly accession version or include 'all' (latest + previous versions)
      --debug                     Emit debugging info
      --exclude-atypical          Exclude atypical assemblies
      --exclude-multi-isolate     Exclude assemblies from multi-isolate projects
      --from-type                 Only return records with type material
      --help                      Print detailed help about a datasets command
      --limit string              Limit the number of genome summaries returned
                                    * all:      returns all matching genome summaries
                                    * a number: returns the specified number of matching genome summaries
                                       (default "all")
      --mag string                Limit to metagenome assembled genomes (only) or remove them from the results (exclude) (default "all")
      --reference                 Limit to reference genomes
      --released-after string     Limit to genomes released on or after a specified date (MM/DD/YYYY)
      --released-before string    Limit to genomes released on or before a specified date (MM/DD/YYYY)
      --report string             Choose the output type:
                                    * genome:   Retrieve the primary genome report
                                    * sequence: Retrieve the sequence report
                                    * ids_only: Retrieve only the genome identifiers
                                     (default "genome")
      --search strings            Limit results to genomes with specified text in the searchable fields:
                                  species and infraspecies, assembly name and submitter.
                                  To search multiple strings, use the flag multiple times.
      --tax-exact-match           Exclude sub-species when a species-level taxon is specified
      --version                   Print version of datasets