JBrowse 1

JBrowse 1.7.0, now with data export, direct BAM display, and much more

November 5, 2012

I am pleased to announce the release of JBrowse 1.7.0, which includes a great many enhancements both large and small. Very exciting!

First, the download links:

  • JBrowse-1.7.0.zip - 2.9M - Includes everything you need to display your data on the web with JBrowse, optimized for loading speed.
  • JBrowse-1.7.0-dev.zip - 27.4M - Primarily for developers. Includes additional developer documentation, developer tests suites, and full copies of Dojo and Dijit. Now for the big new features.

Firstly, JBrowse can now quickly and efficiently display alignment data directly from BAM files over the web, with no need for any intermediate formatting steps. Just put your .bam and .bai files on your web server, add a few lines of configuration to point JBrowse at them, and go! Moreover, JBrowse has two new track types optimized for displaying alignment data: new** "Alignments" track type**, showing basepair differences and insertions between aligned reads and the reference (using a BAM alignment's MD field), and a new FeatureCoverage track type that generates a depth-of-coverage plot from a BAM file (or from any other source of feature data). Many thanks to Thomas Down and his Dalliance Genome Browser project, from which the JBrowse BAM data backend was derived.

The second headline feature of this release is long-awaited support for exporting and saving sequence and annotation data in FASTA, GFF3, bed, bedGraph, and Wiggle formats. Just turn on the track of interest and click on its track label to bring up a new menu of things you can do with that track, one of which is "Save track data". This has been one of the top features users have been requesting for a long time, and now it's finally here!

Third, we have two important enhancements to JBrowse's already-excellent support for BigWig** quantitative data**: a new Wiggle/Density track type, analogous to GBrowse's popular wiggle_density track type, that shows quantitative data using varying intensity of color. Additionally, the existing Wiggle/XYPlot supports a new bg_color option that, if set, provides a background color for all data points in the track, making it easy to **distinguish between regions with no data, and regions with 0-valued data**. Many thanks to Steffi Geisen at the University of Granada for her continued help driving progress on this and many other issues.

Read on for the exhaustive list of changes in this release, including bug fixes, more keyboard navigation enhancements, colored DNA basepairs, more configuration options, and speed enhancements.

1.7.0 2012-11-05 19:22:17 America/New_York

  • Added a new direct-access storage driver for BAM files, removing the need for bam-to-json.pl. This new method of BAM access is far superior to the old bam-to-json.pl in nearly every way, except in browser compatibility. Like the BigWig direct access backend added in JBrowse 1.5.0, it is based on code from Thomas Down's Dalliance Genome Explorer, and works in all major browsers except Internet Explorer, because IE lacks support for the necessary web standards. It may work with Internet Explorer 10, but this has not been tested yet.

  • Added a new Alignments track type designed to work seamlessly with BAM files. This track type shows basepair differences and insertions between aligned reads and the reference, and highlights reads with missing mate-pairs in red.

  • Added the ability to export track data in FASTA, GFF3, bed, bedGraph, and Wiggle formats (issue #104). To export data, turn on the track of interest, then click on its track label to bring up the track menu, and select "Save track data".

  • Added a new Wiggle/Density track type, analagous to the GBrowse wiggle_density glyph type. Shows the Wiggle information using varying intensity of color (issue #66). Renamed the Wiggle track to Wiggle/XYPlot, and made the old Wiggle track type an alias to Wiggle/XYPlot.

  • Both Wiggle/XYPlot and Wiggle/Density now support a style -> bg_color option. Color-density plots blend the pos_color or neg_color into the bg_color in amounts that vary with the wiggle data, and xyplots fill the background color behind all points that have data present, regardless of value. bg_color defaults to off for xy xplots, and semi-transparent gray for density plots. Setting this makes it easier for users to distinguish at a glance between regions with no data, and regions with a value of 0.

  • Added a new FeatureCoverage track type, which shows a dynamically-computed XY-plot of the depth of coverage of features across a genome. One good use of this track type is to provide a quick coverage plot directly from a BAM file. However, since this track calculates coverage on the fly, it can be slow when used with large regions or very deep coverage. In this case, it is recommended to generate a BigWig file containing the coverage data, and display it with a Wiggle/XYPlot or Wiggle/Density track.

  • DNA bases are now displayed with color-coded backgrounds, allowing basepair information to be discerned when zoomed somewhat further out, when base letter cannot be drawn. Colors are also designed to match the base-mismatch colors used in Alignment tracks, enabling clearer SNP visualization.

  • Added a vertical line cursor and labels showing the current basepair position of the mouse when hovering over the scale bar, or when doing a rubber-band zoom (Erik Derohanian) (issue #32).

  • Added an animation to make it easier to see where in the track selection list a closed track has gone, when using the simple track selector (issue #151).

  • Information dialog boxes are now easier to dismiss: clicking anywhere outside of them, or pressing any key, will make them go away.

  • Improvements to feature track configuration:

    *   Feature tracks no longer use the `style.subfeatureScale`

    configuration variable to determine whether to show subfeatures. Instead, subfeatures are shown if the parent feature, when shown on the screen, is wider than style.minSubfeatureWidth, which defaults to 6 pixels. * Make explicitly-configured track labelScale, histScale, and descriptionScale not be modulated by the feature density: only use the feature density to pick the scale defaults

  • The default feature-detail dialog box now shows more information, adding:

    • the feature's exact length
    • full details of its subfeatures

  • Added a locationBoxLength configuration variable that controls the width of the location box. In addition, the default width of the location box is now also smarter. Instead of a fixed 25 characters, it is calculated to fit the largest location string that is likely to be produced, based on the length of the reference sequences and the length of their names.

  • Pressing SHIFT+-up/down arrow keys now cause the genome view to zoom in and out. If ALT is added, it zooms further. Thanks to Karsten Hokamp for the excellent suggestion.

  • Holding SHIFT while scrolling left and right with the arrow keys causes the view to scroll further.

  • Added a theme configuration variable to allow changing the graphical theme to something different from the default "tundra". However, no other themes are implemented yet.

  • Greatly sped up rendering of HTML subfeatures by caching the heights of subfeature HTML elements.

  • Fixed bug in which the genome view executed a double-click zoom when users rapidly clicked on multiple track 'close' buttons.

  • Fixed bug with the genome view scrolling in response to arrow keys being pressed when typing in the location box.

  • Fixed bug in which the score display in Wiggle tracks would sometimes flicker when moving the mouse.

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