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v1

latestOpenAPI 3.0.12026-08-06107337528.9 KB
Genome

Get a genome assembly report by taxon

Get a genome assembly report by taxon. By default, in paged JSON format, but also available in tabular (accept: text/tab-separated-values) or JSON Lines (accept: application/x-ndjson) formats.

get/genome/taxon/{taxons}/dataset_report

Path parameters

taxonsstring[] required

NCBI Taxonomy ID or name (common or scientific) at any taxonomic rank

Query parameters

filters.reference_onlyboolean

If true, limit to reference genome assemblies.

filters.assembly_source'all' | 'refseq' | 'genbank'

Limit to either RefSeq (GCF_) or GenBank (GCA_) genome assemblies.

filters.has_annotationboolean

Limit to annotated genome assemblies.

filters.exclude_paired_reportsboolean

If true, for GenBank (GCA_)/RefSeq (GCF_) pairs, returns the RefSeq copy. When no RefSeq copy exists, the GenBank assembly is returned.

filters.exclude_atypicalboolean

If true, exclude atypical genome assemblies, i.e., genomes that have assembly issues or are otherwise atypical.

filters.assembly_version'current' | 'all_assemblies'

Limit to the most recent (current) version of a genome assembly.

filters.assembly_levelV2reportsAssemblyLevel[]

Limit to genomes at the specified assembly level

filters.first_release_datestring date-time

Limit to genomes released on or after the specified date

filters.last_release_datestring date-time

Limit to genomes released on or before the specified date

filters.search_textstring[]

Limit to genomes that match the specified submitter name, assembly name, infraspecific name (or modifier), or organism name.

filters.is_metagenome_derived'METAGENOME_DERIVED_UNSET' | 'metagenome_derived_only' | 'metagenome_derived_exclude'

Exclude or limit to metagenome-assembled genomes (MAGs).

filters.is_type_materialboolean

If true, limit to genomes derived from type material.

filters.is_ictv_exemplarboolean

If true, limit to genomes derived from an ICTV exemplar (only applies to virus genomes).

filters.exclude_multi_isolateboolean

If true, exclude genomes that were sequenced as part of large multi-isolate projects.

filters.type_material_category'NONE' | 'TYPE_MATERIAL' | 'TYPE_MATERIAL_CLADE' | 'TYPE_MATERIAL_NEOTYPE' | 'TYPE_MATERIAL_REFTYPE' | 'PATHOVAR_TYPE' | 'TYPE_MATERIAL_SYN'

Limit to genomes derived from specific type material categories.

tax_exact_matchboolean

If true, only return assemblies matching the specified taxon, but not child taxa. For example, if querying by "Canis lupus", return Canis lupus but not Canis lupus familiaris genomes.

table_fieldsstring[]
returned_content'COMPLETE' | 'ASSM_ACC' | 'PAIRED_ACC'

Return complete genome assembly reports, or abbreviated reports with assembly accessions with or without paired assembly information.

page_sizeinteger

The maximum number of genome assembly reports to return. Default is 20 and maximum is 1000. If the number of results exceeds the page size, page_token can be used to retrieve the remaining results.

page_tokenstring

A page token is returned when the results count exceeds page size. Use this token along with previous request parameters to retrieve the next page of results. When page_token is empty, all results have been retrieved.

sort.fieldstring
sort.direction'SORT_DIRECTION_UNSPECIFIED' | 'SORT_DIRECTION_ASCENDING' | 'SORT_DIRECTION_DESCENDING'
include_tabular_header'INCLUDE_TABULAR_HEADER_FIRST_PAGE_ONLY' | 'INCLUDE_TABULAR_HEADER_ALWAYS' | 'INCLUDE_TABULAR_HEADER_NEVER'

Specify when to include the table header when requesting a tabular report.

Response

A successful response

content_type'COMPLETE' | 'ASSM_ACC' | 'PAIRED_ACC'
total_countinteger
next_page_tokenstring