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.

[arangrhie]

Hi @DayTimeMouse,

Use all HiFi reads.
Completeness is measured based on num. kmers found in the assembly / found in the reads. That means, if you are using haplotype-specific reads, your denominator will be only half the genome.

Best,
Arang

[DayTimeMouse]

Hi @arang,

But I am still confused about using all HiFi reads to evaluate QV and completeness. Because I want to evaluate each haplotype not primary genome.

[arangrhie]

Run merqury with the two fasta files as input - such as merqury.sh read.meryl hap1.fa hap2.fa out.
The QV file will contain QV for each haplotype and all together (both haplotypes).