JBrowse 2 features

JBrowse 2 was designed to address some shortcomings that were going to be large hacks or difficult to add to the JBrowse 1, and enable brand new modalities such as new view types that can be displayed alongside our linear genome view.

Feature comparison

FeatureJBrowse 2JBrowse 1
Displays status updates during track loading (e.g. Downloading BAM index...)✔️
Uses webworkers for parsing and rendering tracks✔️
Supports interactive editing of configuration in the app✔️
Can "flip" or reverse complement the linear view✔️
Supports htsget✔️
Hi-C data rendering✔️
Can display multiple chromosomes in a single view✔️
Sort read pileup in alignments tracks✔️
Show soft clipping in alignments tracks✔️
Supports new view types such as circular, dotplot, etc.✔️
Connect to UCSC trackHubs✔️ 1
Built in spreadsheet for flipping through variant datasets✔️
Ability for non-admin users to open tracks and share them with others in their session URL✔️

1 Requires that the trackhub host support CORS for the jbrowse-web, jbrowse-desktop does not require this however

New view types

JBrowse 2 also supports things never before really possible in JBrowse 1 such as entirely new "view types" that can be shown alongside other views in the app. This includes:

  • Circos 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

  • Spreadsheet view - Open formats like BED, VCF, CSV, TSV, or even bespoke formats like STAR-fusion in the spreadsheet view

Data format support

Here is a short list of current data format support

  • CRAM/BAM
  • htsget protocol for BAM files
  • VCF (tabixed)
  • GFF3 (tabixed)
  • BED (tabixed)
  • BigBed
  • BigWig
  • JBrowse 1 NCList (backcompat)
  • plain text VCF, BED, CSV, TSV, BEDPE, STAR-fusion output (spreadsheet formats)
  • PAF (synteny/dotplot)
  • Indexed FASTA/BGZip indexed FASTA
  • 2bit
  • .hic (Hi-C contact matrix visualization)