JBrowse 2 feature overview
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 view -
Breakpoint 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 | ✔️ [#footnote-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 | ✔️ [#footnote-2] | ❌ |
| Embeddable directly in React applications | ✔️ [#footnote-2] | ❌ |
| Ability to search by gene name/ID (added in 1.4.0) | ✔️ | ✔️ |
| URL query API e.g. specifying ?loc=chr1:1-100 in URL bar | ✔️ | ✔ ️ |
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 @jbrowse/react-linear-genome-view package).
See the full list of our embedded components here.
Embedded views versus full JBrowse app
Embedded views are intended to facilitate genome browsing within the context of an existing webpage, however if it makes sense for a given use case, one might decide to run an instance of JBrowse on one's hosting website instead. Detailed below are the core differences between embedded components and the full JBrowse app:
| Embedded components [#footnote-3] | JBrowse Web |
|---|---|
| Only has access to one view type | Access to all view types loaded into the JBrowse session, including those from plugins |
| Feature details open as a dialogue | Feature details open as a left/right oriented drawer |
| Only has access to plugin display types and adapters | Access to all plugin extensions (displays, views, adapters, widgets, etc.) |
| No built-in concept of local session, saving or loading | Save / import / export session options for any user |
| Only configured tracks available to view | Various options to populate new tracks from local or remote sources |
Both can:
- enable/disable tracks through the Track interface
- change the track's assembly based on what is available in the configuration
- manipulate the views with zoom, horizontal flip, view all regions, track label positioning, etc.
- change track display options
- export the view as an SVG
Footnote 1
If using with JBrowse 2 web, requires that trackhub server be configured to allow CORS
Footnote 2
See
@jbrowse/react-linear-genome-view on npm
Footnote 3
Note that though the embedded components lack certain functionality, they are designed for web developers to build a custom system around, so though some of these options are not available by default, the ability to design mechanics such as sessions and custom track manipulation is present for a developer seeking to do these things.