To access options affecting the sequence font and background/foreground color, click on the Style panel expand bar entitled Sequence, or choose View > Style > Sequence.
|Select font options for sequence names||Select a font from the Font drop-down menu. Recently selected fonts (if any) appear at the top of the menu, and other available fonts appear below the row of dashes. Enter the preferred font size by typing a number between 4-72 in the box at right, or by using the corresponding up and down arrows ( ).|
|Select font options for tracks||Check the box next to Track names font, then use the corresponding drop-down menu to change the font from the current value. Enter the preferred font size by typing a number between 4-72 in the box at right, or by using the corresponding up and down arrows ( ).|
|Change the sequence color scheme in the Alignment view||To change the letter color in the Alignment view, check the Color sequence foreground box. To change the background color (boxes around each letter), check the Color sequence background box. Then make selections from the corresponding drop-down menus. Color schemes are described in Available color schemes. To specify which parts of the sequence should be colored, see Alignment coloring in the Alignment section below.|
To access options affecting the Alignment view, click on the Style panel expand bar entitled Alignment, or choose View > Style > Alignment.
|Specify the type(s) of editing allowed in an .sqd assembly|| Make a selection from the Editing drop-down menu. Choices are:
|Limit color-coding to the targeted coverage region only||Check the Color only in targeted coverage regions box to cause coloring options selected elsewhere in this section to only be applied to nucleotides in the targeted region of the assembly.|
|Display quality scores|| To display quality scores as subscripts next to each nucleotide, check the Quality box and then make a selection from the drop-down menu to the right:
|Specify where background and foreground coloring should be applied||To show where background and/or foreground coloring should be applied, make a selection from the Alignment coloring drop-down menu. This option is only active if at least one of the Color sequence foreground or Color sequence background boxes are checked in the Sequence section described above. Options include: No special coloring, Color only differences from consensus, Color only matches to consensus, Show only differences from consensus, and Color matches and differences. The last option will apply the foreground and/or background colors to all nucleotides.|
|Display negated weights or trimmed sequence with a custom font color or highlighter||Check the corresponding font color box (left) or highlight box (right) to enable color choosing. Then click on the “A” and/or Color “highlighter” icons to open their color choosers.|
To access options affecting the visibility of reads in the Strategy view, click on the Style panel expand bar entitled Strategy, or choose View > Style > Strategy.
|Show or hide specific types of paired reads in the Strategy view||Choose an option from the Show drop-down menu or manually check or uncheck the individual boxes: Unpaired, Inconsistent (single contig, Inconsistent (multi contig), Consistent (single contig), Consistent (multi contig), Consistent if regrouped, Split. If your group of checked/unchecked boxes does not match any of the presets, the Show menu will automatically change to Custom.|
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