News/JBrowse 1.8.0 released
I am pleased to announce the release of JBrowse 1.8.0, a major new JBrowse release with some great new features, and lots of smaller improvements.
It can be downloaded from http://jbrowse.org/jbrowse-1-8-0/.
The number 1 new feature is: JBrowse can now open local BAM, BigWig, and GFF3 files that reside on the user’s computer, without the need to transfer any data over the network. For example, if a user is viewing a genome in JBrowse 1.8 at her favorite database website, and she has a 20GB BAM file on her computer for that same genome, she can just open her local BAM file and view it alongside the data from the website, without needing to upload the BAM file anywhere. Give this new feature a try, and let us know how it goes! The File->Open dialog works for remote URLs too, or even mixtures of local files and URLs.
There are also two new track types designed for even better display of BAM data:
First, there is the new Alignments2 track type, which is a faster, <canvas>-based track for viewing alignments, including base-level indels and mismatches. It is much more performant when viewing very dense or deep sets of alignments, and is meant to largely replace the HTML-based Alignments track type that was introduced in JBrowse 1.7.0.
Second, there is a new SNPCoverage track, that draws the coverage of alignment features along the genome, along with a graphical representation of SNP distribution, and tables showing frequencies for each SNP. Many thanks to Julien Smith-Roberge, a co-op student at the Ontario Institute for Cancer Research for the initial implementation of this!
SNPCoverage track
The last headline feature, which will be of interest primarily for developers, is the introduction of a new plugin system for JBrowse. It’s still a work in progress, the details of the plugin API will probably not be finalized for a while, but the broad strokes of it are set out on the JBrowse Plugin API page on the GMOD wiki. If you are interested in living on the bleeding edge and developing a JBrowse plugin, contact the gmod-ajax mailing list, or contact me directly.
Happy browsing. ;-)
Robert Buels
Lead Developer
JBrowse - http://jbrowse.org
