The assemblies query method

Refer to interactive documentation : http://enterobase.warwick.ac.uk/api/v2.0/swagger-ui#!/Assemblies

The assemblies query method shows metadata for genome assemblies including N50, coverage, size, and links to FASTA contigs.

An example of this type of query to try in the interactive documentation has "database" set to "senterica", "orderby" set to "barcode", "limit" set to "2", reldate set to "10", "assembly_status" set to "Assembled" and "sortorder" set to "asc" and corresponds to an HTTP request to the URL

 http://enterobase.warwick.ac.uk/api/v2.0/senterica/assemblies?limit=2&reldate=10&assembly_status=Assembled&sortorder=asc

which (at the time of the query) obtained the result

{
  "Assemblies": [
    {
      "assembly_barcode": "SAL_IA5204AA_AS",
      "assembly_status": "Assembled",
      "coverage": null,
      "download_fasta_link": "http://enterobase.warwick.ac.uk/upload/download?assembly_barcode=SAL_IA5204AA_AS&database=senterica",
      "download_fastq_link": "http://enterobase.warwick.ac.uk/upload/download?assembly_barcode=SAL_IA5204AA_AS&database=senterica&file_format=fastq",
      "id": 85204,
      "lastmodified": "2017-05-01T22:02:56.892765+00:00",
      "n50": 406329,
      "top_species": "Salmonella enterica;96.66%",
      "version": 1
    },
    {
      "assembly_barcode": "SAL_KA9491AA_AS",
      "assembly_status": "Assembled",
      "coverage": 58,
      "download_fasta_link": "http://enterobase.warwick.ac.uk/upload/download?assembly_barcode=SAL_KA9491AA_AS&database=senterica",
      "download_fastq_link": "http://enterobase.warwick.ac.uk/upload/download?assembly_barcode=SAL_KA9491AA_AS&database=senterica&file_format=fastq",
      "id": 109491,
      "lastmodified": "2017-04-30T17:32:38.119705+00:00",
      "n50": 276765,
      "top_species": "Salmonella enterica;93.44%",
      "version": 1
    }
  ],
  "links": {
    "paging": {
      "next": "http://enterobase.warwick.ac.uk/api/v2.0/senterica/assemblies?orderby=barcode&limit=2&reldate=10&offset=2&assembly_status=Assembled&sortorder=asc"
    },
    "records": 2,
    "total_records": 412
  }
}

The page about downloading assemblies has an example where metadata is obtained for an assembly via the straindata endpoint which may be more convenient for particular applications.

As noted on that page, it works well to fetch assemblies' metadata via an assemblies query method if you already have assembly barcodes. For example, try an assemblies query in the interactive documentation for the database senterica with "barcode" set to "SAL_IA5204AA_AS" which corresponds to a request to the URL

http://enterobase.warwick.ac.uk/api/v2.0/senterica/assemblies?barcode=SAL_IA5204AA_AS

and obtains the result

{
  "Assemblies": [
    {
      "assembly_barcode": "SAL_IA5204AA_AS",
      "assembly_status": "Assembled",
      "coverage": null,
      "download_fasta_link": "http://enterobase.warwick.ac.uk/upload/download?assembly_barcode=SAL_IA5204AA_AS&database=senterica",
      "download_fastq_link": "http://enterobase.warwick.ac.uk/upload/download?assembly_barcode=SAL_IA5204AA_AS&database=senterica&file_format=fastq",
      "id": 85204,
      "lastmodified": "2017-05-01T22:02:56.892765+00:00",
      "n50": 406329,
      "top_species": "Salmonella enterica;96.66%",
      "version": 1
    }
  ],
  "links": {
    "paging": {},
    "records": 1,
    "total_records": 1
  }
}

Wiki

enterobase-web / api_assemblies

The assemblies query method