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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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No peak. #296

Open paul-bio opened 2 years ago

paul-bio commented 2 years ago

Hello,

from the log file, I could not determine the peak value for --hom-cov. nohup.txt

And this is the code that i used. $hifiasm -o hifiasm -t 80 --hg-size 1.9g -D 10 -l 3 -s 0.4

By the way, I got C : 95%, D : 61% values from BUSCO. It seems assembly is done wonderfully except handling duplications.

Can you give me any suggestions?

Thanks. Paul.

chhylp123 commented 2 years ago

Sorry for the late reply. In most cases, it is caused by the low quality HiFi reads (see https://github.com/chhylp123/hifiasm/issues/93#issue-852259042), no enough coverage, or containments.