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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

FeatureJBrowse 2JBrowse 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
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✔️

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 @jbrowse/react-linear-genome-view package).