How to handle PacBio simulated reads before mapping

[RDorney]

Hello @rrwick, I experienced some poor mapping performance with Minimap2 for reads simulated using the pacbio2016 (only changing depth, mean sequence identity, all other settings as default). I noticed it gets progressively worse when I lower the mean sequence identity (go figure), but reads simulated with nanopore2020 models don't experience this problem.

I've been using this command to align my simulated pacbio reads

minimap2 -ax splice:hq -uf 

I'm just wondering if I was meant to input my pacbio2016 reads into the Iso-seq pipeline prior to mapping with Minimap2?