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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Unexplained assembly error #466

Open justdx opened 1 year ago

justdx commented 1 year ago

Hello, first of all, thank you for developing such a great tool. I'm using Hifiasm (v0.16) to assemble the Arabidopsis genome. The overall performance is pretty good. However, I found some 2-20 bp assembly errors, while the HiFi reads showed a nice consensus pattern (see figure below). May I ask how these errors are included, and is there any solution to eliminate them as much as possible? unknow_error

chhylp123 commented 1 year ago

Sorry for the late reply. It might be the consensus errors of hifiasm, or there are other variants that makes hifiasm hard to perform consensus. As the Arabidopsis genome is haploid, could you please take any polish tool to postprocess hifiasm?

justdx commented 1 year ago

Thank you very much for your reply and advice. However, could you explain to me how Hifiasm achieves reads consensus?