Repeat handling parameters compute a threshold for deciding the number of identical subsequences of bases (mers) used to indicate a putative repeat. Mers that are common to two or more fragment reads are aligned to determine the overall layout of reads. For additional information, see How mer tags are chosen.
Repeat handling is controlled via the Place repeat reads drop-down menu in the Alignment tab. This tab is accessed from the Assembly Options screen by pressing the Advanced Options button, then the Alignment tab.
The repeat threshold can also be computed by multiplying the Match repeat percent parameter value in the Advanced Assembly Options dialog by the Expected coverage. Any mer that occurs more frequently than the computed threshold is not considered for use as a mer tag in determining overlaps. Coverage can be determined in two ways:
- By using the length of the genome/fragment being sequenced, as specified by the Expected genome length parameter in the Assembly Options dialog. If this option is used, SeqMan NGen calculates expected coverage by dividing the Expected genome length value by the total length of all sequences in the project.
- By using a fixed number for expected coverage, as specified by the Expected coverage parameter in the Assembly Options dialog.
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