BaseAssembly

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Built into JBrowse core. View source.

Example usage#

Example: minimal#

A hand-authored human assembly. sequence is a ReferenceSequenceTrack whose adapter points at a bgzipped+indexed FASTA — the uri shorthand auto-resolves the companion .fai/.gzi index files. geneticCodes translates the mitochondrial contig with the vertebrate mitochondrial code (NCBI table 2):

{
  name: 'hg38',
  aliases: ['GRCh38'],
  sequence: {
    type: 'ReferenceSequenceTrack',
    trackId: 'hg38-ref',
    adapter: {
      type: 'BgzipFastaAdapter',
      uri: 'https://example.com/hg38.fa.gz',
    },
  },
  geneticCodes: { chrM: 2 },
}

Example: shorthand-flat#

The flattest form: an assembly is just a name and a sequence-file uri. jbrowse-core picks the adapter (Bgzip/Indexed/TwoBit) from the extension, derives the .fai/.gzi siblings, and fills in the ReferenceSequenceTrack. refNameAliases/cytobands take the same bare { uri } shorthand. (Keep the uri key rather than a bare string so relative URIs still resolve against the config's location.)

{
  name: 'hg38',
  uri: 'https://example.com/hg38.fa.gz',
  refNameAliases: { uri: 'https://example.com/hg38.aliases.txt' },
  cytobands: { uri: 'https://example.com/hg38.cytoBand.txt' },
}

Example: shorthand-sequence#

sequence.type/sequence.trackId are boilerplate that can be omitted — they're always 'ReferenceSequenceTrack' and a name derived from the assembly name — leaving just the adapter (whose own uri shorthand still infers the adapter type and index siblings):

{
  name: 'hg38',
  sequence: { adapter: { uri: 'https://example.com/hg38.fa.gz' } },
}

Example: with-refname-aliases-and-cytobands#

Adds refNameAliases (so chr1 and 1 resolve to the same sequence) and cytobands (ideogram banding), each fetched from its own adapter:

{
  name: 'hg38',
  sequence: {
    type: 'ReferenceSequenceTrack',
    trackId: 'hg38-ref',
    adapter: { type: 'BgzipFastaAdapter', uri: 'https://example.com/hg38.fa.gz' },
  },
  refNameAliases: {
    adapter: {
      type: 'RefNameAliasAdapter',
      location: { uri: 'https://example.com/hg38.aliases.txt' },
    },
  },
  cytobands: {
    adapter: {
      type: 'CytobandAdapter',
      cytobandLocation: { uri: 'https://example.com/hg38.cytoBand.txt' },
    },
  },
}

Example: custom-display-name-and-genetic-codes-sidecar#

Sets a displayName for the assembly selector and loads the per-refName genetic codes from a sidecar TSV (geneticCodesLocation) instead of inlining them — handy when a config generator emits the mapping separately:

{
  name: 'hg38',
  displayName: 'Homo sapiens (hg38)',
  sequence: {
    type: 'ReferenceSequenceTrack',
    trackId: 'hg38-ref',
    adapter: { type: 'BgzipFastaAdapter', uri: 'https://example.com/hg38.fa.gz' },
  },
  geneticCodesLocation: { uri: 'https://example.com/hg38.genetic_codes.tsv' },
}

See the Config slots section below for all available configuration fields.

Overview#

This corresponds to the assemblies section of the config

BaseAssembly - Identifier#

Every BaseAssembly has a unique name, a required top-level field that identifies it (not one of the config slots below).

there is no separate "id" field on an assembly: the "name" is the id, usually a short machine-readable string like hg38. For a longer human-readable label, set the "displayName" config slot instead

Config slots#

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.

pluginManager.getTrackType('ReferenceSequenceTrack')
.configSchema

{ chrM: 2, chrPltd: 11 }

{ uri: 'https://example.com/hg38.genetic_codes.tsv' }

Related links#

• Guide: Assemblies
• Guide: Cookbook