Genome assembly of pacbio reads with SMRT Link
I have been trying to do a genome assembly of a microbial genome around 9Mbp. I am using SMRT Link for the purpose. Can anyone suggest me the best selection of parameters (seed length cutoff, FALCON cfg overrides, seed coverage, minimum concordance) for a good assembly of the genome of that size?
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I will just suggest flye. Did you run it with the default parameters? What was the quality?