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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Phasing #183

Closed m-jahani closed 3 years ago

m-jahani commented 3 years ago

Hi, If a long-running time was okay, what --n-weight, --n-perturb, and --f-perturb would you recommend for the best phasing results? What is the best way to check phasing quality?

chhylp123 commented 3 years ago

If you have trio, you can use trio as ground truth for evaluation. If not, probably you can just use Hi-C heatmap...

As for --n-weight, --n-perturb and --f-perturb, the default value is Ok if your p_utg.gfa has <100k unitigs. It is hard to say if larger values can make the results better. If your p_utg.gfa has too many unitigs, I guess larger values for these options should be helpful.

m-jahani commented 3 years ago

Thanks for your quick answer. My p_utg.gfa has ~10K unitigs. I think I should be okay with the default values.