FIG. 7.

Construction of the conflict graph for five haplocontigs corresponding to “red” and “blue” haplomes and mapped to the consensus graph shown in black (a). Blue and red contigs represent the blue and red haplomes. Contigs 1 and 4 have overlapping alignments (shown by gray dashed lines) but belong to different haplomes and thus are likely to have differences in the overlapping regions (connected by an edge in the conflict graph). Contigs 1 and 5 also have overlapping alignments but coincide in the overlapping region of the alignment. Thus, vertices 1 and 5 in (b) are not connected by an edge. (c) Contigs that are aligned to an edge and that form several intersecting groups. Since it is not possible to separate the haplomes in the entire region, we perform it independently in each region. (d) Contigs from each region forming a connected bipartite subgraph.