Question for Work with hifiasm

[lijl459]

Hello,

I have a question regarding the use of haphic for genome assembly and processing results with hifiasm.

The genome I'm working with is diploid, and the haploid chromosome number is 11. In the command:

haphic pipeline allhaps.fa HiC.filtered.bam nchrs --gfa hap1.p_ctg.gfa,hap2.p_ctg.gfa

should I set nchrs to 11 or 22?

Additionally, what is the difference between this approach and directly using p_utg.fa? Will I obtain haplotype-phased assemblies if I run:

haphic pipeline p_utg.fa HiC.filtered.bam nchrs --gfa p_utg.gfa?

And in this case, should nchrs be set to 11 or 22?

Thank you!