Fig. 1

The steps of the NPGREAT method. Telomere-containing ultralong Nanopore reads are shown as blue line segments with black arrows designating terminal ((TTAGGG)n tracts), and are used to anchor the orientation. These along with ultralong Nanopore reads selected from distal 1-copy subtelomere regions are used as scaffolds upon which the Linked-Read assembly (REXTAL) contigs (red line segments) are placed and corrected. The correction of possible misassemblies within the REXTAL contigs is primarily in Tandem Repeat (TR) regions, where the Nanopore reads have a more accurate representation than the short-read Linked-Read assemblies which typically collapse tandem repeats into a short consensus sequence. Properly positioned, oriented, and corrected REXTAL contigs are merged with nanopore connector segments for the NPGREAT output, a single assembled sequence