Figure 1. The Bionano scaffolding tool does not merge contigs even if they share labels.

Instead, it inserts 13 N’s gap between contigs, thus artificially duplicating the shared region. (A) BiSCoT merges contigs that share enzymatic labelling sites. (B) If contigs do not share labels but share a genomic region, BiSCoT attempts to merge them by aligning the borders of the contigs. (C) The Bionano scaffolding tool does not handle cases where contigs can be inserted into others. BiSCoT attempts to merge the inserted map with the one containing it if they share labels.