Fig. 2

Correction of REXTAL assemblies using Nanopore Reads. A The alignments between the nanopore and the REXTAL sequence reveal a segment whose length in the nanopore read (light blue segment) is different than in the REXTAL contig (light red segment). This indicates a potential region where a deletion has occurred in the REXTAL contig. We identify the exact location of the deletion by obtaining the alignments of the deletion boundary regions in question in unmasked mode. Then, we split the REXTAL contig at those coordinates, filling the missing part with the corresponding nanopore sequence. B In most cases where length differences between nanopore and REXTAL assemblies are seen, the initial alignments between the nanopore read and the REXTAL contig reveal a tandem repeat region better represented in the nanopore read. In these cases, the tandem-repeat pattern sequence is removed from the REXTAL contig and the contig is split at those junctions. The properly aligned segments from the REXTAL contig flanking the TR region are joined with the nanopore sequence containing the tandem repeat to form the NPGREAT assembly