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chhylp123 / hifiasm

Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
MIT License
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kmer coverage #209

Open guptay opened 2 years ago

guptay commented 2 years ago

Hi, I work on a highly heterozygous genome (2.4%). I used the default parameter to run HiFiASM. Based on the k-mer coverage the heterozygous peak is at 38 but HfiASM is using that as a homozygous peak. I have attached the log file here. Could you suggest changing the parameters (--purge-max or -s or --hom-cov) to get the proper phased assembly? I have Hi-C data as well which we can try to incorporate in Hi-C based assembly.

Thanks, Yogesh hifi.v1.log

chhylp123 commented 2 years ago

Can you have a try with '-D10' and '--hom-cov 76'? '-D10' is used for error correction and '--hom-cov 76' is used for post-processing like phasing/purging.