How to deal with extremely high mapping rate?
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oddguyeee commented
I use hifiasm with HiFi reads to construct primary contigs, and scaffolding with 3ddna pipeline. Although I obtain a relatively complete genome, with 92.9% of busco and 95% of primary contigs, the extremely high mapping rate was found by mapping HiFi reads to final assembly. According to log file, the homozygous and heterozygous read coverage threshold were 36 and 18, respectively, as showed in k-mer plot. How can I reset the assembly parameters?
