TwoBitAdapter

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

Example usage#

A .2bit file is self-contained; add chromSizes to skip an initial full-file scan on genomes with many contigs:

{
  type: 'ReferenceSequenceTrack',
  trackId: 'my_assembly-ReferenceSequenceTrack',
  adapter: {
    type: 'TwoBitAdapter',
    uri: 'https://example.com/genome.2bit',
  },
}

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

Related links#

• Track: ReferenceSequenceTrack
• Display: LinearGCContentDisplay
• Display: LinearReferenceSequenceDisplay
• Guide: Assemblies
• Guide: Supported file types

Config slots#

These slots go inside the track's adapter: "adapter": { "type": "TwoBitAdapter", ... }. It also accepts the shorthand keys uri, baseUri, chromSizes 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/default.chrom.sizes', locationType: 'UriLocation' }