I don't know. It will be hard. Minimap2 won't work well at 15% error rate on ~150bp reads. Probably stampy or bwa-mem will work better.

Thanks for the info, Heng. I'll try bwa mem -xont2d. I'll also try first correcting with Racon.

To map nanopore reads to an uncorrected miniasm assembly for Racon, do you suggest minimap2 -xmap-ont?

Perhaps also add -xmap-ont -w5 to increase sensitivity.

I'll try that. Thanks, Heng.

Any luck with either bwa-mem or minimap2?

Rather than align to the uncorrected Miniasm assembly, I used two rounds of Racon correction with the Nanopore reads alone, and then aligned the short reads to the assembly using BWA-MEM. If I try aligning to the uncorrected assembly, I'll post back here. Thanks for your help, Heng.

Hi guys,

I wonder if this was ever sorted. what parameters were used to map short reads to a one-round polished miniasm assembly? Currently racon developper recommends using minimap2 with -x sr parameter, but I can see here that bwa mem should work better, which one would you finally recommend and what parameters should be fine-tuned?
Cheers,