Large gaps closed by long Nanopore reads. (A) Contigs of seven genome assemblies are aligned with Chromosome I of the N2 reference (see layouts for all chromosomes in Supplemental Fig. S2). The respective red and blue thick lines show alignments of contigs in the plus and minus strands. The vertical red line shows a large gap that failed to be filled by seven genome assemblies. (B–D) Examples of provisional gap closure using Nanopore data for a region where a long gap was found. (B) A self-dot plot for an initial model in which we ligate the last 30 kb of sequence from a contig just before a gap on Chromosome I (colored red) to 30 kb of sequence from another contig just after that gap. Two black boxes represent long tandem repeat expansions around the gap. (C) A dot plot between a single 92,790-nt Nanopore read (green) that connects the gap and the simple ligation model in B. (D) A self-dot plot of the Nanopore read shows that the two tandem repeats in C were underestimated. In this example, the left tandem repeat (red asterisk) has 1130 copies of a 26-nt unit string (5′-CATTTTTCTAAAATCCGCCGCAATGC-3′). Supplemental Table S4 shows the units of all tandem repeats in five large assembly gaps.
