Adjusting parameters for regular Pacbio Sequel II CLR reads

Hello,

I am trying to construct the human ChrX centromere as demonstrated in your paper, except with reads from our own sample: 87X of regular Pacbio Sequel II CLR reads (N50=28.3k, 10X of >50k reads). May I ask what are the parameters that I should adjust besides the ones below?

error-mode=pacbio min-coverage=2 coverage=3

Thanks for creating such a valuable tool, Tim

Hi Tim,

Thank you for your interest in centroFlye. It is difficult to tell what the parameter selection will be optimal without seeing the data. I suggest to select different parameters and check the resulting assemblies. You can use VerityMap to validate the resulting assembly https://github.com/ablab/VerityMap. Having said that, I am not actively maintaining centroFlye as I switched to assembly using more accurate HiFi reads with LJA assembler https://github.com/AntonBankevich/LJA. Sorry that I can't be more of help.

Andrey