Fig. 9

Hi-C links between the two haplotypes after the gene binning step for the Nanopore Guppy v4 and Guppy v5 assemblies. Hi-C links within scaffold bins are excluded. The phasing signal between scaffold bins in both Nanopore assembly is weak with only ~5 Mb of each haplotype have more than 80% of their Hi-C contacts to the same haplotype. This indicates the presence of extensive phase switches. In contrast, the HiFi assemblies show a phasing signal similarly to the Pgt assembly with phase switches present (Fig. 5)