text: user6459: 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
  
  user77: 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.
  
original_text: 6459: <p>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 ?</p>
  
  <p>Thanks</p>
   77: <p>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.</p>
  