Figure 4

Modeling constraints on the contig connectivity graph. (A) For two contigs i and j connected through mate pairs, the quantity J _ij encodes the information about relative orientation (sign of J _ij ) and number of mate pairs connecting those contigs (absolute value of J _ij ). Minimizing the energy produces an orientation assignment that satisfies as many constraints as possible. The constraints that are not satisfied in the optimal configuration (shown in red) are ignored in the next part. (B) To determine the relative position of contigs, we model the collection of mate pairs connecting contigs i and j as a spring attached to the start points of those contigs. The relaxed length of this spring, , is equal to the average suggested distance between the start points of those contigs given by mate pair constraints.