Figure 5

Detecting and resolving scaffold mis-assembly using density profile and Potts model. (A) Two scaffolds, shown in green and magenta, belong to the different regions of the genome. Mis-assembly of a chimeric contig composed of contig 3 from the green scaffold and contig 7 from the magenta scaffold causes the two distinct scaffolds to join together. In the new scaffold, many positions are covered by two contigs. (B) For a genuine scaffold, the density profile (see text for definition) should be close to one (or zero for gaps). The plot shows the density profile for a mis-assembled scaffold obtained in the assembly process of a real dataset from the E. coli genome. Each point along the x-axis represents a window of length 1000 bases along the scaffold. The y-axis shows the average density for positions located within each window. From this profile, we can infer that at least four scaffolds have been mis-assembled together. (C) Our labeling method for dividing contigs into distinct groups for the case shown in (A) can lead to any of the three possibilities shown here. We use color to present different labels. Note that the problematic contig (3-7) always lies at the boundary between different groups.