Fig. 5

Scaffolding of repeat sequences with OPERA-LG. a The correctness and completeness (Repeats in Scaffold) of scaffolding with repeat contigs in OPERA-LG. A set of contigs is considered correctly placed in a gap if the contigs belong to that gap and if they are in the right order and orientation. For completeness, all repeat contigs (longer than 500 bp) in valid gaps (gaps where the adjacent contigs are in the right order and orientation) and with edges in the scaffold graph were considered. b Length distribution of gaps with contigs placed by OPERA-LG in various genomes. c, d Results from evaluating whether various gap-filling methods can substitute for OPERA-LG: c Percentage of gaps filled and d percentage of correctly filled gaps by different gap-filling methods in scaffold gaps where OPERA-LG correctly placed a repeat contig. SEALER was unable to run to completion after 10 days