ChromSizesAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the sequence plugin. View source.

Example usage#

{
  type: 'ReferenceSequenceTrack',
  trackId: 'my_assembly-ReferenceSequenceTrack',
  adapter: {
    type: 'ChromSizesAdapter',
    uri: 'https://example.com/species.chrom.sizes',
  },
}

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

loads only chromosome names and lengths from a UCSC-style .chrom.sizes file (tab-separated name<TAB>length), with no actual sequence. Useful for karyotype or whole-genome/synteny views where the base-level sequence isn't needed.

Related links#

• Track: ReferenceSequenceTrack
• Display: LinearGCContentDisplay
• Display: LinearReferenceSequenceDisplay
• Guide: FromConfig adapters
• Guide: Supported file types
• Guide: Synteny visualization (OrthoFinder orthogroups)

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "ChromSizesAdapter", ... }. 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.

{ uri: '/path/to/species.chrom.sizes', locationType: 'UriLocation' }