How will Hifiasm handle sex chromosomes for the heterogametic gender? I’m planning on doing a pseudohaplotype assembly on a male (XY) specimen’s genome. Will I get a primary and alternate assembly for both sex chromosomes, or will it somehow recognize that there aren’t second copies of those chromosomes?
Welcome, @AndyCarter
From what I know, there isn’t any special handling for sex chromosomes. I could be wrong!
To learn more I would
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Start here Hifiasm — hifiasm 0.16.0 documentation
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Maybe ask at a scientific forum? Biostars or Seqanswers come to mind.
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Test it out and see what happens! The first link has example data to play around with.
Others are welcome to add more, and it would be great if you want to post back what you find out, either from somewhere else or your own tests. 
Thanks Jennifer. I posted questions on both the forums you mentioned, and sent an email to the corresponding author of the 2021 Hifiasm paper listed on the Hifiasm documentation page you linked. Hopefully someone will chime in. If I don’t get an answer that way, I’ll test it myself and see what I get. Either way, I’ll report back on my post as you suggested. Thanks for the leads!
Andy
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