Fig. 2.

Diploid assembly of a pair of homologous supercontigs. Shown is a pair of homologous supercontigs (10065 and 20065) built from phrap contigs 1563, 2303^*, 998, 2231, and 1981, where ^* denotes sequence complementation. There are terminal alignments indicating separately assembled homologous regions occurring between 1563:2303^*, 998:2303^*, 2303^*:2231, and 2231:1981. For simplicity, both diverged homologs are shown in pink. In nearly homozygous regions of the phrap assembly, where a single sequence represents both homologs, sequence is copied in the direction shown by the arrows to fill in the dotted regions in the opposite homologous supercontig, reversing the process described in Fig. 1. In the heterozygous regions, low-quality bases at the ends of phrap contigs corresponding to the small blue regions in Fig. 1 b and c are also replaced with sequence from the other homolog. Not shown is a small region of internal trimming in contig 998 (see Supporting Text).