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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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how to evaluate switch error rate without trios data #193

Open jinxin112233 opened 2 years ago

jinxin112233 commented 2 years ago

Hi Due to the lack of trio data, we used HiFi + HiC to complete the assembly of the haplotype. For the evaluation of switch error rate, most pipelines require trio data. Let's ask if there is a pipeline that can complete the evaluation of the switch error rate without trio data.

Best Jinxin

lh3 commented 2 years ago

You can't reliably evaluate phasing errors without additional data types. The best you can do is to compare to HapCUT2 phasing, but without other data types, you don't really know which tool is more correct even if you see differences.