Fig. 2.

Errors in the overlap graph. (i) Cycles in graphs from linear genomes. False edge (red) connects two nodes within the same component and creates a cycle. In graphs built for circular genomes, cycles arise naturally, but graphs from linear genomes should not contain cycles. (ii and iii) False edges. Orientation inconsistent false edge (ii, red edge) creates an orientation conflict when placing a map in the graph in a particular orientation. False edges that do not introduce orientation conflict (iii, red edge) can spuriously connect maps from unrelated genomic regions. (iv) Chimeric maps. Chimeric maps (D) combine maps from at least two different genomic regions (shown in blue and orange), resulting in falsely connected regions.