Best practice for preprocessing Nanopore reads

[Luisagi]

First of all, congratulations on that fantastic tool for its speed.

I am not sure if "fastp" automatically detects adapters used by ONT libraries. And what would be the recommended flags to treat this kind of reads obtained by ONT?

[tseemann]

Probably better to use porechop followed by filtlong

[dsurujon]

I've also started using Guppy's trimming and quality filtering options during basecalling. @tseemann I'd love to hear your opinion on this vs porechop