JBrowse 2 feature overview
One of the biggest features of JBrowse 2 is the ability to have multiple views on the same screen, or to compose multiple views together (e.g. a synteny view combines multiple single linear genome views)
Example showing multiple views on the same screen, an alignments track on top
and a long read vs reference comparison with the "synteny" view
For more screenshots see the gallery
New view types#
JBrowse 2 supports creating new "view types" that can be shown alongside other views in the app. Importantly, these can be added by third-party plugins.
The view types available by default with JBrowse 2 web include
Circular view - Used to show whole genome overview of chromosomal translocations. The VCF breakend
<BND>and<TRA>type features can be rendered as arcs across the viewBreakpoint split view - Our breakpoint split view shows the connection between long split alignments or paired end reads across multiple chromosomes using stacked linear genome views
Dotplot view - Zoomable comparison of whole genome alignments or synteny datasets
Linear synteny view - Another option for exploration of syntenic alignments using stacked linear genome views
Tabular view - Open formats like BED, VCF, CSV, TSV, or even bespoke formats like STAR-fusion in the tabular view
Feature comparison#
| Feature | JBrowse 2 | JBrowse 1 |
|---|---|---|
| Status updates during track loading (e.g. Downloading BAM index...) | ✔️ | ❌ |
| Sort, color, and filter by BAM/CRAM tags and other advanced options | ✔️ | ❌ |
| Uses webworkers for parsing and rendering tracks | ✔️ | ❌ |
| Supports interactive editing of configuration in the app | ✔️ | ❌ |
| Can "flip" or reverse complement the linear view | ✔️ | ❌ |
| Hi-C data rendering | ✔️ | ❌ |
| Can display multiple chromosomes in a single view | ✔️ | ❌ |
| Sort read pileup in alignments tracks | ✔️ | ❌ |
| Show soft clipping in alignments tracks | ✔️ | ❌ |
| Built-in tabular view for datasets | ✔️ | ❌ |
| Can open UCSC track hubs | ✔️ 1 | ❌ |
| Add and remove plugins without running scripts | ✔️ | ❌ |
| Non-administrator users can open tracks and share them with others | ✔️ | ❌ |
| Embeddable in JavaScript projects using NPM | ✔️ 2 | ❌ |
| Embeddable directly in React applications | ✔️ 2 | ❌ |
| Name searching e.g. ability to type a gene name/ID to search for it | ❌ | ✔️ |
| URL query API e.g. specifying ?loc=chr1:1-100 in URL bar | ❌ | ✔️ |
1 If using with JBrowse 2 web, requires that trackhub server be configured to allow CORS
2 See @jbrowse/react-linear-genome-view on npm
Supported data formats#
Here is a short list of data formats supported in core JBrowse 2. Plugins are available for additional data formats.
- CRAM
- BAM
- htsget
- VCF (Tabix-indexed)
- GFF3 (Tabix-indexed)
- BED (Tabix-indexed)
- BigBed
- BigWig
- JBrowse 1 nested containment lists (NCLists)
- plain text VCF, BED, CSV, TSV, BEDPE, STAR-fusion output (tabular formats)
- PAF (synteny/dotplot)
- Indexed FASTA/BGZip indexed FASTA
- 2bit
- .hic (Hi-C contact matrix visualization)
Integration and embedding#
The JBrowse 2 platform and plugins are designed from the ground up to be modular and reusable. For example, individual JBrowse 2 views (e.g. linear, circular, tabular, etc) can be packaged to be embeddable in other web applications (as demonstrated by the JB2 Linear genome view.