Figure 2

DNP walking. Manual repeat resolution is carried out by starting with a read and locating other reads with the same DNP pattern. The repeat group is extended to the right and left by locating reads with the same DNPs at the ends of the reads. In this simple example, the two top reads constitute the beginning of a repeat group. The group is extended by identification of the same DNP pattern in the left end of the two bottom reads. This can be done by eye or searching the alignment for reads with the same DNP ID.