Error correcting PacBio reads prior to alignment with bwa mem

Question

[aindap]

I have PacBio reads of my organism of interest that I would like to align to a reference sequence pulled from GenBank. Does it make sense to error correct and trim the PacBio reads, with a tool like canu and then align with bwa mem?

Answer 1

[Charles Warden]

I would say it is OK to use CCS reads, where it might be a good idea to impose 5x or 10x cutoffs (the default is 3x).

I'm not as certain about error-corrected subreads if the library size is too large to define CCS reads. I guess it should be OK, but I can't really provide you with evidence from 1st hand experience either way. I think of that as mostly an internal step for de novo assembly.