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this is a very general question about diploid genome assembly. I am wondering how people deal with heterozygous region in a genome when assembling ? Do they pick one of the haplotype to be in the referene and leave out the other ? I am particularly thinking about situation similar to mammalian chromosome Y. Do you put Y or X in the assembly ? An hybrid ?

Thanks

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Generally a single allele is used. This may be arbitrary or match the major allele frequency of the species. For sex chromosomes, usually both/all are included, so for mammals both X and Y are part of the reference genome.

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  • $\begingroup$ In order to do so, do they perform "haplotype phasing" ? So, if you have something similar to sexual chromosome on another pair (really big divergent regions), one of them will be left out, as it is not recognise as a particular pair ? $\endgroup$
    – LauraR
    Nov 6, 2019 at 10:04
  • $\begingroup$ There is usually nothing special done in this regard unless it's a more finished genome (mouse, human, etc.). $\endgroup$
    – Devon Ryan
    Nov 6, 2019 at 10:05

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