What mapping software to use for the Racon input (minimap or bwa mem or smth else) and what parameters to choose? I have tried several options and experience errors with ONT 1.1 GB data and Shasta or Flye assembled contigs. What software to choose for FASTQ and BAM or PAF Racon input preprocessing if required? Thank you.
for mapping ONT reads I suggest you to use minimap2, as it is specially designed for long reads; the default options should work fine. Which kind of errors did you get? Could you send an error report?