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Top level links:
- Main top level page for all documentation
- EnteroBase Features
- Registering on EnteroBase and logging in
- Tutorials
- Using the API
- About the underlying pipelines and other internals
- How schemes in EnteroBase work
- FAQ
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 } }
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