Fig. 3

a–f Comparison of NPGREAT and SHASTA subtelomere assemblies with the CHM13 reference genome using QUAST. To assess the quality of the NPGREAT and SHASTA assemblies for each of the selected subtelomeres, we used the QUAST software [17] and the Icarus genome viewer [18], comparing each assembly with the distal-most regions of the selected telomeres (from the end of the telomere (TTAGGG)n tract through the segmental duplication region and into the start of the 1-copy sequence on the centromeric side of the respective subtelomere) in the CHM13 genome sequence (Fig. 3a–f). For each of these figures, the distal segment of reference sequence is indicated by the line segment at the top of the figure; the telomere (TTAGGG)n tract (red) is represented at the left end of each figure representing the p-arms of chromosomes, and the right end of those figures representing the q-arm, with the segmental duplication regions adjacent to (TTAGGG)n represented in green. The purple rectangle corresponds to the NPGREAT assembly, and the blue line segments below represent the Nanopore-only assemblies using SHASTA set for the indicated coverage parameters. The dark blue line segment for each figure represents the SHASTA assembly using the recommended parameters. Nucleotide sequence similarity of each assembly to the reference sequence segment it is aligned with is shown at the right of the respective assembly. a 9p subtelomeric region. There are no misassemblies in either NPGREAT or SHASTA. All assemblies are composed of one contig within this region. b 10p subtelomeric region. SHASTA 2, 3, and 4 have misassemblies (designated as vertical gaps in the figure) in the telomere repeat tract area. SHASTA 3 and 4 also have a local misassemblies designated with a vertical line at 73 kb. All assemblies are composed of one contig. c 18p subtelomeric region. SHASTA 3 has one local misassembly (designated with a vertical line) at approximately 230 kb. All assemblies are composed of one contig. d 19q subtelomeric region. SHASTA 3 and 4 have misassemblies within the telomere repeat tract area; except for these, all assemblies are composed of one contig. e 20p subtelomeric region. SHASTA 2 has one local misassembly (designated with a gap at 105 kb). All assemblies are composed of one contig. f 22q subtelomeric region. The NPGREAT assembly has a local misassembly designated with a gap at 120 kb corresponding to a LINE/L1 element. The SHASTA 2 has two misassemblies within the (TTAGGG)n tract, and SHASTA 4 has a local misassembly at 164 kb. All assemblies are composed of one contig