Fig 3. Overview of the SAMBA scaffolding algorithm.
The method resolves the initial graph into three final contigs, C1-C2-B1-B3-C3-C4 (S4), C5-R-C8 and C6-R-C7. The repeat contig R is duplicated in the final output. Note that if there were no proper edge between contigs C5 and C8, then the final output would contain C5 and C8 standalone instead of C5-R-C8.