JBrowse 2 feature overview

View types

JBrowse 2 supports multiple view types that can be shown simultaneously in the app. Third-party plugins can also add new view types.

• Linear genome view - The primary view for browsing genomic data along a reference sequence. Supports multiple tracks, zooming, navigation, and split view for comparing two regions simultaneously

• Circular view - Whole genome overview of chromosomal translocations. VCF breakend <BND> and <TRA> features are rendered as arcs across the genome

• Breakpoint split view - Shows the connection between long split alignments or paired-end reads across chromosomes using stacked linear genome views

• Dotplot view - Zoomable comparison of whole genome alignments or synteny datasets

• Linear synteny view - Exploration of syntenic alignments using stacked linear genome views

• SV inspector - Spreadsheet-like view of structural variants with a linked circular overview for visual context

• Tabular view - Open BED, VCF, CSV, TSV, or bespoke formats like STAR-fusion output in a sortable, filterable table

What’s new in JBrowse 2

JBrowse 2 was rebuilt from the ground up, with a primary focus on synteny and structural variant visualization that JBrowse 1 could not support, while also expanding on many other capabilities. The table below highlights what is new.

Feature	JBrowse 1	JBrowse 2
Multiple simultaneous view types	✗	✓
Circular / dotplot / synteny views	✗	✓
Structural variant visualization (breakpoint split view, circular arcs)	✗	✓
Hi-C contact matrix	✗	✓
Web worker and WASM speed optimizations	✗	✓
Sort, color, and filter alignments by BAM/CRAM tag	✗	✓
Large database of pre-loaded species	✗	✓
In-app plugin store	✗	✓
UCSC track hub support 1	✗	✓
SVG export of the current view	✗	✓
Embeddable as React / NPM components 2 3	✗	✓

See the demos and gallery for more examples of what JBrowse 2 can do.

Supported data formats

Core JBrowse 2 supports the following formats. Plugins extend this list further.

• Indexed FASTA / BGZip indexed FASTA
• 2bit
• BAM / CRAM
• htsget
• VCF (Tabix-indexed or plain text)
• GFF3 (Tabix-indexed or plain text)
• BED (Tabix-indexed or plain text)
• BigBed
• BigWig
• .hic (Hi-C contact matrix)
• JBrowse 1 nested containment lists (NCLists)
• CSV, TSV, BEDPE, STAR-fusion output (tabular view)

Synteny and dotplot formats

• PAF
• Chain
• Delta
• Pairwise indexed format (PIF)
• MCScan (Python version)

Integration and embedding

The JBrowse 2 platform and plugins are designed from the ground up to be modular and reusable. Individual views (linear, circular, tabular, etc.) can be packaged as embeddable components for other web applications, as demonstrated by @jbrowse/react-linear-genome-view.

See the full list of embedded components.

Footnotes

1. Requires the trackhub server to allow CORS ↩

2. See @jbrowse/react-linear-genome-view on npm ↩

3. See the full list of embedded components ↩