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Filling gaps in supercontigs. (A) Contigs A and B are connected by a path p of contigs X1, …, Xk. The distance dp(A,B) between A and B (along the path p) is the length of the sequence in the path that does not overlap A or B. (B) Contigs Y1 and Y2 share forward-reverse links with the supercontig S. These links position them in the vicinity of the gap between A and B. Therefore, Y1 and Y2 will be used as possible stepping points in the path closing the gap from A to B.
