Fig. 8

Contig coverage of haplotype-specific reads for HiFi assemblies at varying levels of genome coverage. Illumina reads were binned into haplotype-specific reads if they align better to one of the haplotypes from the HiFi chromosomes. These haplotype-specific reads were then re-mapped to the contigs of the downsampled HiFi assemblies as well as to the Nanopore and HiFi-hifiasm assembly. The proportion of each contig covered by reads specific to haplotypes A and B is shown. The HiFi assembly at 40×–50× genome coverage have a clear phasing signal with a relatively low number of contigs containing phase switches, whereas assemblies below 30× coverage have many phase switches