Strategy Viewing and Coverage parameters

Parameters in the Strategy Viewing and Coverage dialog impact coverage graph coloring in the Strategy view and tabular coverage data in the Contig Coverage report.

To access the dialog, use Project > Project Parameters. Click on the phrase Strategy Viewing and Coverage on the left.

• Maximum expected coverage – The maximum coverage expected at any position in the assembly. Positions/ranges above this value will be indicated as “Coverage above maximum” in the Contig Coverage report. In the Strategy view, areas meeting or exceeding this maximum value will be indicated by thick, red areas in the Coverage histogram. The Maximum expected coverage value must be greater than the Coverage threshold value. The default is 100.

• Coverage threshold – The minimum coverage required to be considered sufficient. Positions/range below this value will be indicated as “Below coverage threshold” in the Contig Coverage report. For random sequencing projects, coverage of five to tenfold is commonly desired. However, if you are using the Trace Evidence method to call the consensus, you may well achieve the accuracy you seek with coverage of only threefold. The default is 4.

• Minimum number on each strand – The minimal number of reads on each strand required to be considered sufficient. Positions/ranges where either strand is below this value will be indicated as “Only one strand” in the Contig Coverage report. The default value is 2.