Steps for detecting and filling gaps. (A) Contigs are ordered along the N2 reference assembly. Parts shown as dangling (colored light orange) fail to align and are missing in the N2 reference. (B) At a gap, regions in two Canu contigs (orange) map to proximal loci on the N2 reference; however, the two contigs have dangling end subsequences missing in the reference. In such cases, we estimate gaps between the contigs according to steps illustrated in C–G. (C) A single contig in other assemblies (yellow) fills a gap. (D) A long contig in other assemblies combines multiple contigs separated by more than one gap. (E) More than one contig fills a gap. (F) A single error-corrected read (light blue) fills a gap. (G) A hybrid approach of using multiple contigs and error-corrected reads fills a gap.