I've assembled a known E. coli genome only using nanopore reads. I want to check if the genes predicted matches the ground truth. I tried Prokka but it predicts way too many CDS (~10000). Although most of them are 'hypothetical proteins' so I'm guessing those are false positive ORFs caused by frameshifts as a result of nanopore's systemic indel errors.
Are there programs that work well specifically with nanopore erros in mind? Glimmer and GeneMark both have long histories but I'm guessing they're optimized for short reads.