User guide
General usage
- Basic usage - Navigation, searching, opening files, and common UI controls
- Connections - UCSC track hubs and JBrowse 1 data directories
Track types
- Alignments track - BAM/CRAM pileup and coverage displays
- Feature sequence panel - Sequence extraction for selected features
- Hi-C track - Contact matrix display
- Multi-quantitative tracks - Multiple signal tracks displayed together
- Multi-sample variant displays - Population-level variant views
- Quantitative tracks - BigWig/BedGraph signal tracks
- Sequence track - Reference sequence display
- Variant tracks - VCF variant display
Views
- Dotplot view - Whole-genome synteny dotplot
- Linear synteny view - Linear alignment of two genomes
- SV inspector view - Structural variant spreadsheet and circular view
- Structural variant visualization - Interpreting SV signals across display types
Other features
- Bookmark widget - Saving and sharing genomic locations
- Plugin store - Installing community plugins
Tutorials
- Analyzing a phased trio - Examine inheritance patterns and variant phasing in a trio dataset
- Visualizing DNA methylation - Per-read and aggregate methylation from ONT and modkit
- Multi-sample SV visualization w/ 1kG - Inspect population-level SVs, explore a family trio, and characterize a large chromosomal inversion
- Cancer Genome in a Bottle (SVs) - Load and inspect structural variants from real cancer sequencing data
- Synteny visualization and genome alignment - Compare genome assemblies using dotplot and linear synteny views