Note: This topic is not applicable to BAM-based projects.
To select a reference sequence following an assembly, first select the sequence from the Project Summary window, the Alignment View, or the Strategy View. Then, select Sequence > Mark Reference Sequence. The specified sequence becomes the reference and it appears at the top of each view with its name in italics. If the contig containing the sequence already had a reference sequence, it is no longer the reference.
To de-select a sequence as the reference, select Sequence > Unmark Reference Sequence. The sequence is no longer the reference and it appears among the other sample sequences with its name in plain text.
Note: When a sequence is marked as a reference, its endpoints are automatically set to exactly span the assembled contig.