How do researchers account for heterozygosity in genome assembly? 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
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.