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I am a bioinformatics rookie. I read a paper, it said:

existing algorithms either collapse heterozygous alleles into one consensus copy or fail to cleanly separate the haplotypes to produce high-quality phased assemblies.

So what does it mean to collapse heterozygous alleles?

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I suspect this means that either the multiple alleles are represented with an ambiguity code:

Haplotype1:      ATCG
Haplotype2:      ACCG

Consensus:       AYCG

Or, that from a pile up of mapped reads, the "consensus" is simply called as the allele with the majority of reads.

Read1:     ATCG
Read2:     ATCG
Read3:     ATCG
Read4:     ATCG
Read5:     ATCG
Read6:     ACCG
Read7:     ACCG
Read8:     ACCG
Read9:     ACCG

Consensus: ATCG

Without more context, the meaning is unclear.

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    $\begingroup$ It would be better to not answer bioinformatics questions with no biological component on this site. It is also best to not answer questions that show no evidence of the expected prior research — this encourages sloppiness on the part of posters and results in an accumulation of poorly formed questions that will be of no use to future users. Note that if you feel compelled to put phrases like "I suspect" into your answer this is a strong indication that the question isn't clear enough — in such cases asking for and awaiting clarification is likely to lead to higher quality posts. $\endgroup$
    – tyersome
    Jul 22 at 4:26
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    $\begingroup$ @Darlingtonia - good answer. Regarding the other comment, it's bad enough to be discouraging to newcomers, but must it now also be discouraged for someone to give a helpful and informative answer? Based on the logic that helping one curious novice might lead others to come, or that bioinformatics has nothing to do with biology? It would be much more useful to have a folder or tag system to segregate high- versus low-level questions, as some other forums use. $\endgroup$ Jul 23 at 21:06
  • $\begingroup$ @tyersome This looks like a typical case where a novice can waste a lot of time trying to find an answer where a more experienced professional can quickly provide a relevant explanation. That said, the original poster could have provided more clues about their previous research efforts. Regarding the absence of biological component in the question, we may add that the question might have been better placed in bioinformatics.stackexchange.com $\endgroup$
    – bli
    Aug 1 at 11:32

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