JBrowse 1.5.0 released, includes direct BigWig access!

I’m very pleased to announce the release of JBrowse 1.5.0! There are three headline features in this release. First, we’ve integrated a direct-access BigWig data backend, adapted from the Dalliance Genome Explorer that can read wiggle data directly from compressed BigWig files stored on your web server. Second, there is now a beautiful, full-featured canvas-based Wiggle track type. Third, we have a very powerful new click system that allows JBrowse administrators complete flexibility in configuring what happens when a user left- or right-clicks a feature in an HTML-based feature track, including right-click context menus.

A demonstration of JBrowse 1.5.0 showing a test BigWig-based wiggle track (alongside an old-style image-based wiggle track for comparison) can be seen here, and a whole-genome RNA-seq profile of tomato, with corresponding gene models, can be seen here.

As usual, this release comes in two flavors: the “minimal” release (JBrowse-1.5.0-min.zip – 2.8M) that includes only the software and documentation necessary to format your own data and run the browser, and the “full” release (JBrowse-1.5.0-min.zip – 27.2M) that includes the developers’ test suite, more sample data files, and developer documentation.

Here is the full list of new improvements in 1.5.0:

  • Added a direct-access storage driver for BigWig data files, based
    on code from the Dalliance Genome Explorer by Thomas Down. BigWig
    file access is supported now by the current versions of all major
    browsers except Internet Explorer (which is expected to work when
    version 10 is released along with Windows 8).

  • Added a canvas-based wiggle track implementation for quantitative
    data that, when used with the new BigWig storage backend, removes
    the need to pre-generate rendered images of wiggle data. Its
    display is also highly configurable, with configuration options
    modeled on the GBrowse wiggle_xyplot glyph type
    (i.e. Bio::Graphics::Glyph::wiggle_xyplot).

  • Added highly configurable behavior for left-clicking and
    right-clicking features in HTML-based feature tracks. If a
    menuTemplate option is specified in the track configuration,
    right-clicking a feature brings up a context menu, the items in
    which can be configured to do nearly anything, but that are easy to
    configure for the very common use case of wanting to display
    content from a certain URL. Feature left-clicks are also
    configurable using the same mechanism. Thanks to Alexie
    Papanicolaou and Temi Varghese for the initial implementation of
    context menus.

  • Improved the default HTML feature left-click dialog box. It is now
    both prettier, and more comprehensive, displaying all available
    data for the feature.

  • Added a small helper script, add-track-json.pl that developers
    and advanced users can use to programmatically add a block of track
    configuration JSON to an existing JBrowse configuration file.

  • Improved / fixed vertical alignment of sub-elements of HTML
    features, including subfeatures and the arrowheads that show
    strand. All elements in a feature are now vertically centered by
    default.

About Robert Buels

JBrowse Lead Developer
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