genome

print a summary of a genome dataset

Name

datasets summary genome - print a summary of a genome dataset

Description

Print a summary of a genome dataset by assembly accession, bioproject accession or taxon. The summary is returned in JSON format.

Refer to NCBI’s command line quickstart documentation for information about getting started with the command-line tools.

Examples

  datasets summary genome accession GCF_000001405.39
  datasets summary genome taxon mouse
  datasets summary genome taxon human --assembly-level chromosome,complete_genome
  datasets summary genome taxon mouse --search C57BL/6J --search "Broad Institute"

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 genome
      --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

Fields

MnemonicName
annotinfo-busco-completeAnnotation Info BUSCO Complete
annotinfo-busco-duplicatedAnnotation Info BUSCO Duplicated
annotinfo-busco-fragmentedAnnotation Info BUSCO Fragmented
annotinfo-busco-lineageAnnotation Info BUSCO Lineage
annotinfo-busco-missingAnnotation Info BUSCO Missing
annotinfo-busco-singlecopyAnnotation Info BUSCO Single Copy
annotinfo-busco-totalcountAnnotation Info BUSCO Total Count
annotinfo-busco-verAnnotation Info BUSCO Version
annotinfo-featcount-gene-non-codingAnnotation Info Count Gene Non-coding
annotinfo-featcount-gene-otherAnnotation Info Count Gene Other
annotinfo-featcount-gene-protein-codingAnnotation Info Count Gene Protein-coding
annotinfo-featcount-gene-pseudogeneAnnotation Info Count Gene Pseudogene
annotinfo-featcount-gene-totalAnnotation Info Count Gene Total
annotinfo-nameAnnotation Info Name
annotinfo-release-dateAnnotation Info Release Date
annotinfo-report-urlAnnotation Info Report URL
annotinfo-sourceAnnotation Info Source
assminfo-accessionAssembly Accession
assminfo-bioproject-lineage-accessionAssembly BioProject Lineage Accession
assminfo-bioproject-lineage-parent-accessionsAssembly BioProject Lineage Parent Accessions
assminfo-bioproject-lineage-titleAssembly BioProject Lineage Title
assminfo-biosample-accessionAssembly BioSample Accession
assminfo-blast-urlAssembly Blast URL
assminfo-descriptionAssembly Description
assminfo-genbank-assm-accessionAssembly GenBank Accession
assminfo-levelAssembly Level
assminfo-linked-assmAssembly Linked Assembly
assminfo-nameAssembly Name
assminfo-paired_accessionAssembly Paired Accession
assminfo-refseq-assm-accessionAssembly RefSeq Accession
assminfo-refseq-categoryAssembly Refseq Dategory
assminfo-sequencing-techAssembly Sequencing Tech
assminfo-submission-dateAssembly Submission Date
assminfo-submitterAssembly Submitter
assminfo-typeAssembly Type
assminfo-ucsc-assm-nameAssembly UCSC Assembly Name
assmstats-contig-l50Assembly Stats Contig L50
assmstats-contig-n50Assembly Stats Contig N50
assmstats-gaps-between-scaffolds-countAssembly Stats Gaps Between Scaffolds Count
assmstats-gc-countAssembly Stats GC Count
assmstats-number-of-component-sequencesAssembly Stats Number of Component Sequences
assmstats-number-of-contigsAssembly Stats Number of Contigs
assmstats-number-of-scaffoldsAssembly Stats Number of Scaffolds
assmstats-scaffold-l50Assembly Stats Scaffold L50
assmstats-scaffold-n50Assembly Stats Scaffold N50
assmstats-total-number-of-chromosomesAssembly Stats Total Number of Chromosomes
assmstats-total-sequence-lenAssembly Stats Total Sequence Length
assmstats-total-ungapped-lenAssembly Stats Total Ungapped Length
breedBreed
common-nameCommon name
cultivarCultivar
ecotypeEcotype
isolateIsolate
organelle-assembly-nameOrganelle Assembly Name
organelle-bioproject-accessionsOrganelle BioProject Accessions
organelle-descriptionOrganelle Description
organelle-infraspecific-nameOrganelle Infraspecific Name
organelle-submitterOrganelle Submitter
organelle-total-seq-lengthOrganelle Total Seq Length
organism-nameOrganism name
sexSex
strainStrain
tax-idTaxonomic ID
wgs-contigs-urlWGS contigs URL
wgs-project-accessionWGS project accession
wgs-urlWGS URL

Commands


accession

print a summary of a genome dataset by assembly accession

taxon

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

Generated October 14, 2021