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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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Whether unitig will be filtered based on the hic signal of unitig #666

Open qz1024 opened 1 month ago

qz1024 commented 1 month ago

Hi, I used bwa mem to compare hic data to p-utg files and did some filtering on the results. It was found that there were very few hic signals on some short unitigs. I would like to ask whether hifiasm will filter out unitig nodes with few hic signals in the process of generating conitg from unitig using hic. Looking forward to your reply, wish you a happy life！

chhylp123 commented 1 month ago

No, it won't do any filter for the unitig.

qz1024 commented 1 month ago

Thank you for your answer. I have one more question. What about unitigs whose length is so short that they do not map on the hic data. Or, does the alignment based on kmer not result in misalignment or very little signal. Looking forward to your reply