Figure 2

The Hawkeye Scaffold View. The scaffold view displays the insert panel, outlined with a yellow border, consisting of (a) plots of statistical information, (b) scaffolded contigs, (c) feature tracks, and (d) inserts. Also displayed are the (e) overview panel, (f) control panel, and (g) details panel. The insert panel displays the details and individual inserts for regions of the scaffold selected in the overview panel, whereas unselected regions are grayed out in the overview. By default, inserts are colored by category (green→happy, blue→stretched, yellow→compressed, purple→singleton). The eye is drawn to the cluster of compressed mates towards the bottom of the insert panel.