The purpose of this menu is to configure the operation of the contig editor. Settings can be saved using the "Save settings" button, which also saves preferences for the editor width and height and the location of the divider between the names and sequence panels. It does not save tag macros though; these may be saved separately using the "Save Macros" option. Settings for the following options can be changed.
Sequences have an "X" location in the editor defined by the location within the contig that they align to. The "Y" location though is determined by the sequence layout algorithm, governed by the Pack Sequences setting and Group Readings options.
By default sequences are grouped into distinct technologies, typically with longer sequences up the top (capillary) and shorter ones at the bottom (Illumina, SOLiD). Within these technology groups the sequences are then sorted by their start location, so the top-most sequences start earlier and the bottom most sequences start later.
The Group Readings menu allows user control over these primary and secondary collating orders. The sorting methods are defined below.
This toggles between the normal sequence display (showing the current base assignments) and one in which those assignments that differ from the consensus are highlighted. It makes scanning for problems by eye much easier.
Several modes of highlighting are available: "By dots" will only display the bases that differ from the consensus, displaying all other bases as full stops if they match or colons if they mismatch but are poor quality. The definition of poor quality here can be adjusted using the "Set quality threshold" option of the Settings menu. The base colours are as normal (ie reflecting tags and quality).
Highlight disagreements "By foreground colour" and "By background colour" displays all base characters, but colours those that differ from the consensus. Bases which differ by are below the difference quality threshold are shaded in light blue while high quality differences are dark blue. This allows easier visual scanning of the context that a difference occurs in, but it may be wise to disable the displaying of tags (hint: control-Q toggles tags on and off).
Finally the "Case sensitive" toggle controls whether upper and lower case bases of the same base type should be considered as differences.
This controls whether the editor allocates one row per sequence or whether it is permitted to pack multiple sequences onto a single row, assuming they do not overlap.
The latter allows for a more compact plot which is desirable when dealing with short sequences, however it has the side effect that the reading names can no longer be listed in the names panel to the left.
Sometimes we need to see the background shading underneath an annotation, for example to see the base quality or if we have Highlight Disagreements turned on using the by background colour mode. This option simply hides all annotations from display until it is selected again to reveal them once more.
The Control-Q keyboard shortcut has the same effect.