/genbank/assemblies/search

POST /api/genbank/assemblies/search

Price: 20 credits

List genome assemblies for an organism, with quality and completeness filters

How to use it

Lists every genome assembly NCBI holds for an organism. `taxon` takes a taxonomy id, a scientific name or a common name interchangeably, and always includes the subtree below it - so a genus returns its species' assemblies too. Both archive copies of one assembly are separate rows unless you set `assembly_source`, which is usually what you want when counting genomes. `reference_only` narrows to the single designated reference and is the way to answer 'the' genome of a species. Only the current version of each assembly is listed unless `assembly_version` is set to all_assemblies; `search_text` is how you reach an assembly by its name, such as GRCh38.

Parameters

• access-token string required

Request body

• timeout integer — Max scrapping execution timeout (in seconds) (default: 300; min: 20; max: 1500)
• taxon string required — Organism to list assemblies for: an NCBI taxonomy id, a scientific name or a common name. The whole subtree below it is included (examples: "9606", "Homo sapiens", "human", "Escherichia coli", "562"; minLength: 1)
• count integer required — Number of assemblies to return (min: 1; max: 5000)
• search_text string nullable — Free-text match against the assembly name, accession, submitter and isolate, which is how a named assembly such as GRCh38 is reached (examples: "GRCh38", "T2T-CHM13")
• assembly_version string nullable — Which versions to list: only the current version of each assembly, or every version including the superseded ones. Defaults to the current version (one of: "current", "all_assemblies")
• assembly_levels array nullable — Filter by how finished the assembly is (any-of) (one of: "complete_genome", "chromosome", "scaffold", "contig")
• assembly_source string nullable — Filter by which archive holds the assembly: the RefSeq copy, the GenBank copy, or both (one of: "refseq", "genbank", "all")
• reference_only boolean — Return only the reference assembly designated for the taxon (default: false)
• has_annotation boolean — Return only assemblies that carry a gene annotation (default: false)
• exclude_atypical boolean — Drop assemblies NCBI flagged as atypical for their taxon (default: false)
• first_release_date string nullable — Return only assemblies first released on or after this date (YYYY-MM-DD) (examples: "2020-01-01")

Response

• @type string (default: "GenbankAssembly")
• id string required
• accession string (default: "")
• paired_accession string (default: "")
• source_database string (default: "")
• name string (default: "")
• description string (default: "")
• level string (default: "")
• status string (default: "")
• assembly_type string (default: "")
• diploid_role string (default: "")
• refseq_category string (default: "")
• synonym string (default: "")
• comments string (default: "")
• release_date string (default: "")
• submitter string (default: "")
• assembly_method string (default: "")
• sequencing_technique string (default: "")
• blast_url string (default: "")
• organism string (default: "")
• common_name string (default: "")
• taxid string (default: "")
• strain string (default: "")
• isolate string (default: "")
• cultivar string (default: "")
• ecotype string (default: "")
• breed string (default: "")
• sex string (default: "")
• is_atypical boolean (default: false)
• atypical_warnings array (default: [])
• genome_notes array (default: [])
• suppression_reason string (default: "")
• type_material string (default: "")
• type_material_label string (default: "")
• biosample_accession string (default: "")
• bioproject_accession string (default: "")
• bioprojects array (default: [])
  • @type string (default: "GenbankAssemblyBioProject")
  • accession string required
  • project_title string (default: "")
  • parent_accessions array (default: [])
• paired_assembly object nullable
  • @type string (default: "GenbankPairedAssembly")
  • accession string (default: "")
  • status string (default: "")
  • annotation_name string (default: "")
  • changed_components string (default: "")
  • is_different boolean (default: false)
  • differences string (default: "")
  • manual_diff string (default: "")
  • only_genbank string (default: "")
  • only_refseq string (default: "")
• linked_assemblies array (default: [])
  • @type string (default: "GenbankLinkedAssembly")
  • accession string required
  • assembly_type string (default: "")
• stats object nullable
  • @type string (default: "GenbankAssemblyStats")
  • total_sequence_length integer nullable
  • total_ungapped_length integer nullable
  • chromosome_count integer nullable
  • contig_count integer nullable
  • contig_n50 integer nullable
  • contig_l50 integer nullable
  • scaffold_count integer nullable
  • scaffold_n50 integer nullable
  • scaffold_l50 integer nullable
  • gaps_between_scaffolds_count integer nullable
  • component_sequence_count integer nullable
  • organelle_count integer nullable
  • atgc_count integer nullable
  • gc_count integer nullable
  • gc_percent number nullable
  • genome_coverage string (default: "")
• annotation object nullable
  • @type string (default: "GenbankAssemblyAnnotation")
  • name string (default: "")
  • provider string (default: "")
  • release_date string (default: "")
  • report_url string (default: "")
  • method string (default: "")
  • pipeline string (default: "")
  • software_version string (default: "")
  • status string (default: "")
  • gene_counts object nullable
    • @type string (default: "GenbankGeneCounts")
    • total integer nullable
    • protein_coding integer nullable
    • non_coding integer nullable
    • pseudogene integer nullable
    • other integer nullable
  • busco object nullable
    • @type string (default: "GenbankBusco")
    • lineage string (default: "")
    • version string (default: "")
    • complete number nullable
    • single_copy number nullable
    • duplicated number nullable
    • fragmented number nullable
    • missing number nullable
    • total_count integer nullable
• organelles array (default: [])
  • @type string (default: "GenbankOrganelle")
  • description string required
  • total_sequence_length integer nullable
  • submitter string (default: "")
• average_nucleotide_identity object nullable
  • @type string (default: "GenbankAverageNucleotideIdentity")
  • taxonomy_check_status string (default: "")
  • match_status string (default: "")
  • category string (default: "")
  • comment string (default: "")
  • submitted_organism string (default: "")
  • submitted_species string (default: "")
  • best_match object nullable
    • @type string (default: "GenbankAniMatch")
    • assembly string (default: "")
    • organism_name string (default: "")
    • category string (default: "")
    • ani number nullable
    • assembly_coverage number nullable
    • type_assembly_coverage number nullable
  • submitted_match object nullable
    • @type string (default: "GenbankAniMatch")
    • assembly string (default: "")
    • organism_name string (default: "")
    • category string (default: "")
    • ani number nullable
    • assembly_coverage number nullable
    • type_assembly_coverage number nullable
• checkm object nullable
  • @type string (default: "GenbankCheckm")
  • version string (default: "")
  • marker_set string (default: "")
  • marker_set_rank string (default: "")
  • species_taxid string (default: "")
  • completeness number nullable
  • completeness_percentile number nullable
  • contamination number nullable
• additional_submitters array (default: [])
  • @type string (default: "GenbankAdditionalSubmitter")
  • submitter string required
  • chromosome_name string (default: "")
  • molecule_type string (default: "")
  • bioproject_accession string (default: "")
  • genbank_accession string (default: "")
  • refseq_accession string (default: "")
• wgs_project_accession string (default: "")
• wgs_master_url string (default: "")
• wgs_contigs_url string (default: "")
• url string (default: "")

Errors

• 422 — The request body did not validate Check the fields against this schema. A URN with the wrong prefix is the most common cause.
• 408 — The request ran past its time limit Raise `timeout` in the request body, up to the maximum this endpoint documents. Lowering `count` or turning off the `with_*` flags also helps, because less work finishes sooner.
• 412 — The entity was not found, or a precondition failed Retrying will not help: either the entity does not exist, or the input points at a different one.
• 429 — Too many requests: a rate limit or a usage window is exhausted When the response carries an X-Retry-After header, wait that many seconds and retry: the same number is in the body as `detail.retry_after`, and the limit clears once that window passes. The message in the body names the limit that was hit.
• 500 — Something broke on our side Retrying will not help. If it keeps happening, send us the X-Request-ID from the response headers.
• 529 — Rate limit reached, or the endpoint is overloaded Wait at least 30 seconds, then retry.

Response headers

• X-Error — Error message text (present only on error)
• X-Request-ID — Unique request identifier
• X-Execution-Time — Execution time in seconds
• X-Result-Count — How many records the body carries. 0 means an empty result, which is a normal answer and not by itself an error. A non-zero count can come back together with X-Error when the failure happened partway through — read this header and X-Error independently.
• X-Total-Available-Results — How many records exist for this query, when the endpoint can say. On a `dry_run` request this is the answer and the body is empty. It saturates: the endpoint's documented maximum means 'at least that many', any smaller number is exact.
• X-Warning — Present when the request body carried keys this endpoint does not document. They were ignored, so any filter you meant to apply through them did not apply. Check the spelling against this schema and retry.
• X-Retry-After — Seconds to wait before retrying. Present only on 429.