Our consensus calculation algorithms use the data for all the unclipped bases covering each position in a contig. However, some assembly engines may leave the ends of readings unaligned, and these unaligned bases could therefore lead to the production of an incorrect consensus. The two clipping methods described here (which are available from the gap4 Edit menu) are designed to overcome this potential problem.
In addition to improving the reliability of the consensus calculation, clipping in this way tidies up the alignments, so helping the user to concentrate on the better data. It is important to note that in no case is the clipped sequence thrown away. The contig editor can show this hidden data, and the clip points may be manually adjusted to reveal any clipped sequence.