Mitigate Overlapping Sequence Assignments in Haplotypes

[xuxingyubio]

Hi
I've encountered an issue when assembling the MHC region using individual HiFi data. I noticed that some sequences are assigned to both hap1 and hap2. For instance, hap1 assembled two different alleles for HLA-DRB1, but one of these alleles also appeared in hap2, meaning that an additional allele was assigned to hap1. Is there any method or strategy that could mitigate the occurrence of such a situation?

[chhylp123]

It might be harder. Does hifiasm assemble two different alleles for HLA-DRB1 into one contig?

[xuxingyubio]

The two different alleles for HLA-DRB1 are assembled on different contigs.

[chhylp123]

I see. Then it might be harder since MHC is quite challenge.