LinearSyntenyDisplay

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

Draws a SyntenyTrack in a LinearSyntenyView, as ribbons joining the aligned regions of two stacked linear genome views.

Example usage#

A SyntenyTrack config to paste into tracks. The adapter needs the query (first) and target (second) assembly names, matched by the track's assemblyNames. See the synteny track guide for all options:

{
  type: 'SyntenyTrack',
  trackId: 'hg38_vs_mm10',
  name: 'hg38 vs mm10',
  assemblyNames: ['hg38', 'mm10'],
  adapter: {
    type: 'PAFAdapter',
    uri: 'https://example.com/hg38_vs_mm10.paf',
    queryAssembly: 'hg38',
    targetAssembly: 'mm10',
  },
}

Related links#

• Adapter: BlastTabularAdapter
• Adapter: ChainAdapter
• Adapter: DeltaAdapter
• Adapter: MashMapAdapter
• Adapter: MCScanAnchorsAdapter
• Adapter: MCScanBlocksAdapter
• Adapter: MCScanSimpleAnchorsAdapter
• Adapter: MultiGenomeIndexedPAFAdapter
• Adapter: MultiGenomePAFAdapter
• Adapter: MultiPairwiseSyntenyAdapter
• Adapter: PAFAdapter
• Adapter: PairwiseIndexedPAFAdapter
• State model: runtime API
• Config guide: Tracks
• Developer guide: Custom track and display types

Retired keys#

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