Exploring structural variation using JBrowse by Richard Finkers
Latest Release – JBrowse 1.12.0
- 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.
- Can run as a stand-alone app on OSX and Windows.
JBrowse Overview Screencast (January 16, 2013 – JBrowse 1.7.6)
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.
JBrowse development is funded by the NHGRI.
If you use JBrowse in a project that you publish, please cite the most recent JBrowse paper, which is here in Genome Research.
JBrowse is released under the GNU LGPL or the Artistic License, see the JBrowse LICENSE file.