NcbiSequenceReportAliasAdapter

Auto-generated from the config schema in the source — see the config guide for concepts. Provided by the config plugin. View source.

Example usage#

Goes on an ASSEMBLY, under refNameAliases — not on a track. The file ships beside any RefSeq assembly on NCBI datasets and aliases the RefSeq, GenBank and UCSC-style names of every sequence at once, so it replaces a hand-maintained chromAlias table:

{
  name: 'GCF_000001405.40',
  sequence: {
    type: 'ReferenceSequenceTrack',
    trackId: 'GCF_000001405.40-ReferenceSequenceTrack',
    adapter: {
      type: 'BgzipFastaAdapter',
      uri: 'https://example.com/GCF_000001405.40.fa.gz',
    },
  },
  refNameAliases: {
    adapter: {
      type: 'NcbiSequenceReportAliasAdapter',
      uri: 'https://example.com/GCF_000001405.40_sequence_report.tsv',
    },
  },
}

Example: keeping the FASTA's own names#

With an NCBI FASTA (NC_000001.11), the default displays UCSC-style names (chr1) while still fetching bases under the accession. Set useNameOverride: false to display the accessions instead, with chr1 left searchable as an alias:

{
  name: 'GCF_000001405.40',
  sequence: {
    type: 'ReferenceSequenceTrack',
    trackId: 'GCF_000001405.40-ReferenceSequenceTrack',
    adapter: {
      type: 'BgzipFastaAdapter',
      uri: 'https://example.com/GCF_000001405.40.fa.gz',
    },
  },
  refNameAliases: {
    adapter: {
      type: 'NcbiSequenceReportAliasAdapter',
      uri: 'https://example.com/GCF_000001405.40_sequence_report.tsv',
      useNameOverride: false,
    },
  },
}

Reads refName aliases for an assembly from an NCBI sequence_report.tsv file.

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "NcbiSequenceReportAliasAdapter", ... }. It also accepts the shorthand keys uri, baseUri in place of writing a location slot out. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

Retired keys#

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.

Related links#

• Tutorial: Synteny visualization (OrthoFinder orthogroups)
• Developer guide: RefName aliasing