Pseudohaplotype assembly with Hifiasm and sex chromosomes from XY specimen
I'm planning to do a pseudohaplotype assembly with Hifiasm on PacBio HiFi wgs data for an XY male specimen. Does anyone know how Hifiasm will handle the sex chromosomes? I mean, will it give me primary and alternate assemblies for the sex chromosomes even though there aren't two copies of those chromosomes? How will it handle the pseudoautosomal regions of homology between the X & Y? Is there a strategy I should be using to limit the mess I make of the sex chromosomes? I'm new to all of this, so pretend I'm 8 years old.
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