The Alignment tab is used to set parameters for the alignment phase of the assembly. To access the tab from the Preassembly Options screen, click the Advanced Options button then click on the Alignment tab.
Default parameters vary according to the sequencing technology and project type specified elsewhere in the wizard, and values seldom need to be changed.
|Gap penalty||The penalty for opening or extending a gap during an alignment. This penalty is deducted from the pairwise score used to calculate match percentage. A high gap penalty suppresses gapping, while a low value promotes gapping.|
|Maximum gaps||The theoretical maximum length of a gap that could be inserted. In practice, the maximum gap size will usually be about half of this value. The maximum allowable value is 99.|
|Mismatch penalty||The penalty for a base mismatch during an alignment. This penalty is deducted from the pairwise score used to calculate match percentage.|
|Match window||The size of the window used to calculate match percentage.|
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