chhylp123
commented
2 years ago - How does Hifiasm assigns contigs which have only one copy in the diploid, such as Y-chromosome-linked-contigs?
Hifiasm will assign X chromosome and Y chromosome into different haplotypes. We think it is what users want.
- Can Hifiasm use Hi-C data to phase such contigs from sex chromosomes or corresponding autosomes
Yes, it can. But if the contigs are extremely repetitive and fragmented, hifiasm may have mistakes.
Hello, @chhylp123
I have used Hifiasm combined with the Hi-C technology to assembly one male mammal genome, this great software is fast and high-efficiency, but I have some questions about the haplotigs of Hifiasm.
The first question is How does Hifiasm assigns contigs which have only one copy in the diploid, such as Y-chromosome-linked-contigs? Does Hifiasm assigns these contigs to two haplotigs? Or assigns Y-chromosome-linked-contigs to one haplotig (paternal), while assigns X-chromosome-linked-contigs to another haplotig (maternal)? I see the haplotig1 is ~150 Mb larger than haplotig2, I think these contigs were assigned according to their parents, but I have no idea about it.
The second question is If the sex chromosome is relative young, which means it is similar as some parts of autosomes or its counterpart, can Hifiasm using Hi-C data to phase such contigs from sex chromosomes or corresponding autosomes? Or assemly such contigs as one? From my opinion, even these sex-chromosome-linked-contigs are similar as these from autosomes or counterpart, the Hi-C interaction between them is very different.
I see the website say "Hifiasm can purge duplications between haplotigs without relying on third-party tools such as purge_dups", so is it necessary to purge again using other purge tools such as purge_haplotigs after the Hifiasm phasing (Heterozygosity ~2%)?
Looking forward to your reply.