Pilon does not use the long reads to call the middle base of a CCxGG motif,
as the ONT base calls can be confused by methylation.
If your library went through rounds of PCR, or you are sequencing an organism that doens't have CpG methylation, we don't want to skip those motifs in correction.
If your library went through rounds of PCR, or you are sequencing an organism that doens't have CpG methylation, we don't want to skip those motifs in correction.
Can it be made a
--skip-ccxggswitch?