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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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No peak for the heterozygous read coverage #207

Open aboersch opened 3 years ago

aboersch commented 3 years ago

I applied hifiasm to create a de novo assembly using HiFi reads sequenced from the genome of a diploid human cell line. When I checked the log file (attached), I see only one peak for the homozygous read coverage. The heterozygous one is not present. I was wondering, why it happened, and my only guess is the read coverage, which is around 10. Did you have an experience with processing samples of low coverage and getting this kind of histogram? hifiasm_asm.log

chhylp123 commented 3 years ago

Yes, low coverage might be the reason. And the heterozygous peak might be filtered out as sequencing errors by '--min-hist-cnt'. See https://github.com/chhylp123/hifiasm/issues/49 and https://hifiasm.readthedocs.io/en/latest/parameter-reference.html. But for your case, it should be caused by low coverage.