Figure 3

Small contigs. An example of a region in containing smaller contigs. There are 5 possible paths to connect c₁ and c₆. The highest scoring one is [c₁,c₄,c₅,c₆], with $\left(\sum _{i}g\left(c_i\right),\sum _{i}b\left(c_i\right)\right)=(44,10)$, giving π _p = 34 and it is the selected path between c₁ and c₆. In this path the good edges are represented as solid lines and bad edges are represented as dotted lines. A lower-score alternative is [c₁,c₂,c₄,c₅,c₆] with (g(c _i ),b(c _i ))=(47,18), giving π _p = 29. c₂ is a problematic contig that can be chimeric or consists of repeated sequence(s). The three remaining paths, all of them with negative score, are [c₁,c₂,c₃,c₈,c₆],[c₁,c₄,c₆],[c₁,c₂,c₄,c₆].