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Table 2 JBrowse plugins

From: JBrowse: a dynamic web platform for genome visualization and analysis

Plugin name Plugin description
RegexSequenceSearch Allows the user to enter a simple sequence motif of regular expression, then creates a new feature track showing matches to this motif. Illustrates implementation of JBrowse menu extensions and popups (with CSS), creation of a new track, access of the reference sequence, and dynamic creation of features based on client-side computation
NeatHTMLFeatures Extends HTMLFeatures tracks to render introns using the standard cartoon representation of a “hat”-shaped elbow line and features with gradient “tube” effect. Illustrates the implementation of custom glyphs. Draws the intron using Scalable Vector Graphics (SVG)
NeatCanvasFeatures The analog of NeatHTMLFeatures for CanvasFeatures tracks
HideTrackLabels Extends the toolbar to implement a new button that hides track labels. Illustrates the implementation of toolbar buttons
DebugEvents Logs all milestone and globally published events to the browser’s JavaScript console. Illustrates the use of plugins for debugging and subscription to dojo/topic events
CategoryUrl Adds a new ‘category’ URL parameter that displays all tracks in a particular category. Illustrates the implementation of new URL parameters
PubAnnotation Allows JBrowse to display text annotations from PubAnnotation. Illustrates the creation of a new feature store that queries an external repository
  1. The plugins in this table are included in the JBrowse source distribution, in many cases for expository purposes. Other plugins may readily be developed and added to any given JBrowse installation