Table 7 Proportion of false-positive Hi-C contacts between haplotypes in the Nanopore assemblies. Only Hi-C reads with high mapping quality (MAPQ > 30) were used in this analysis. Over half of all trans Hi-C contacts in the Nanopore Guppy v4 assembly are false-positive signals between haplotypes. The Nanopore Guppy V5 assembly has a slightly lower false-positive signal, which is still substantially higher than in the HiFi assemblies (Table 2)

From: Physical separation of haplotypes in dikaryons allows benchmarking of phasing accuracy in Nanopore and HiFi assemblies with Hi-C data