Answers.Body: <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>
  
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Answers.CreationDate: 2019-11-06T10:04:39.947Z
Answers.Text: 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 ?
Answers.UserDisplayName: LauraR
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-11-06T10:05:38.150Z
Answers.Text: There is usually nothing special done in this regard unless it's a more finished genome (mouse, human, etc.).
Answers.UserDisplayName: Devon Ryan
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Answers.CreationDate: 2019-11-06T09:54:41.963Z
Answers.LastActivityDate: 2019-11-06T09:54:41.963Z
Answers.UserDisplayName: Devon Ryan
Body: <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>
  
Tags: <reference-genome><genome-sequencing>
Title: How do researchers account for heterozygosity in genome assembly?
ThreadText: # How do researchers account for heterozygosity in genome assembly?
  
  (Asked by: username_0 on 2019-11-06)
  
  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
  
  **Tags:** reference-genome, genome-sequencing
  
  
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  ## 1 answers
  
  ### Answer by username_1 on 2019-11-06. Score: 1 | Accepted answer
  
  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.
  
  > **Comments:**
  > **username_0**: 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 ?  
  > **username_1**: There is usually nothing special done in this regard unless it's a more finished genome (mouse, human, etc.).  
  
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