Alignment Viewer is a viewer editor that displays the primary analysis result of GT and executes secondary analysis etc.
Alignment Viewer can be launched from GT's main window.
The Alignment Viewer consists of a menu bar, a tool box, and four panes.
Although the menu bar is fixed in the Viewer window, the toolbox and the four panes can be removed from the window and displayed at any position on the desktop.
The toolbox can also be hidden.
The four panes are named as Navigation Pane, Feature Pane, Consensus Pane and Fragment Pane from the top.
Navigation Pane is a special pane for navigating the other three panes and has a two-step scale of genome-wide scale and scale within the selected region.
Feature Pane has functions similar to IMC's main feature map and can perform most functions of IMC.
Consensus Pane is a function to display the Assembly result as a sequence alignment of Contig and Read constituting it, and a function to display the Mapping result as a sequence alignment of the reference genome sequence and Read.
Fragment Pane is a function to graphically display Consensus Pane, which allows you to view assemblies and mapping in a more bird's-eye view.