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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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hifiasm for only ONT reads #573

Open cahuparo opened 9 months ago

cahuparo commented 9 months ago

Hi @chhylp123,

I was wondering if hifiasm can run without PacBio Hifi reads. I only have Ultra long ONT reads and I am wondering if the newer flag (-ul) would work in such a case. Thanks!

-Camilo

chhylp123 commented 9 months ago

Sorry for the late reply as I was quite busy last month. If you are using traditional ONT data, the answer is no. However, hifiasm may work with the latest ONT reads: https://labs.epi2me.io/gm24385_ncm23_preview/.

wrengs commented 3 months ago

Hi Camilo, Another strategy, if you have enough coverage, might be to first correct the ONT data with Herro ( https://github.com/lbcb-sci/herro ). Thereafter you could "chop" the error corrected data to ~30kb followed by running Hifiasm and even include >50kb ONT reads as UL.