Fig. 3: Comparison of HG002 assemblies with the HG002 T2T Q100 reference across the SMN1 and SMN2 region.
From: Efficient near-telomere-to-telomere assembly of nanopore simplex reads
Each plot, generated using SVbyEye40, shows minimap238 alignment results of the assemblies to the annotated SMN1 and SMN2 regions within the HG002 Q100 reference. Alignments corresponding to the same contig are shown in the same colour. For consistency, several contigs aligned to the reverse-complement strand—such as the orange contig in Fig. 3b—are shown in their original orientations. Alignments of hifiasm (ONT) are shown above the reference, and alignments of Verkko + HERRO are shown below. The positions of SMN1 and SMN2 in the HG002 Q100 reference are highlighted in pink and yellow, respectively. a, HG002 paternal assemblies using ONT standard simplex reads. b, HG002 maternal assemblies using ONT standard simplex reads. c, HG002 paternal assemblies using ONT ultra-long simplex reads. d, HG002 maternal assemblies using ONT ultra-long simplex reads.
