evaluation for QV in haplotypes

[DayTimeMouse]

Hi,

Thank you for developing this nice tool.

I have obtained hap1.fa and hap2.fa using hifiasm(HiFi +HiC reads). Next, I would like to evaluate the QV and completeness of each haplotype.

However, I am uncertain about which reads to use to build the meryl databases. Should I use haplotype-specific reads or all HiFi reads?

When I use all HiFi reads to assess the QV and completeness of each haplotype, the QV is 48, and the completeness is 90.26%. In contrast, when I use haplotype-specific reads, the QV is 36, and the completeness is 99.40%.

Best regards.