The JBrowse Genome Browser

JBrowse is a fast, embeddable genome browser built completely with JavaScript and HTML5, with optional run-once data formatting tools written in Perl.

Featured Post

Exploring structural variation using JBrowse by Richard Finkers

Latest Release – JBrowse 1.11.4

Note: BAM, VCF, and BigWig tracks not available on Internet Explorer 9 and earlier.

Headline Features

  • Fast, smooth scrolling and zooming. Explore your genome with unparalleled speed.
  • Scales easily to multi-gigabase genomes and deep-coverage sequencing.
  • Supports GFF3, BED, FASTA, Wiggle, BigWig, BAM, VCF (with tabix), REST, and more.  BAM, BigWig, and VCF data are displayed directly from chunks of the compressed binary files, no conversion needed.
  • Includes an optional “faceted” track selector (see demo) suitable for large installations with thousands of tracks.
  • Very light server resource requirements. In fact, JBrowse has no back-end server code, just tools for formatting data files to be read directly over HTTP. Serve huge datasets from a single low-cost cloud instance.

JBrowse Overview Screencast (January 16, 2013 – JBrowse 1.7.6)

Browser Compatibility

The latest release of JBrowse is tested to work with the following web browsers:

  • Mozilla Firefox (10 and later)
  • Google Chrome (17 and later)
  • Apple Safari (5 and later, 6 required for BAM, BigWig, VCF+Tabix)
  • Microsoft Internet Explorer (9 and later, 10 required for BAM, BigWig, VCF+Tabix)

Server-side code, which is used only to pre-generate static data files (no CGI), requires only BioPerl and a few other CPAN modules. The result is a cross-platform AJAX genome browser that is easy to install, embed and customize.

JBrowse is a GMOD project.

Funding

JBrowse development is funded by the NHGRI.

Citing JBrowse

If you use JBrowse in a project that you publish, please cite the most recent JBrowse paper, which is here in Genome Research.

License

JBrowse is released under the GNU LGPL or the Artistic License, see the JBrowse LICENSE file.