Question: clip vc clip-nanopore?

[spock]

I have a dazzler database with a combination of PacBio and Nanopore reads. Which of the clip options is more suitable in this case? Thank you in advance :)

[govinda-kamath]

I'd suggest clip-nanopore as the nanopore reads have more correlated errors, which could lead to mis-assemblies.

We've never bench-marked on any such data-sets though. Are there any publicly available data-sets with a combination of pacbio and nanopore reads?

[spock]

Thanks a lot for a quick response! I'll try clip-nanopore.

This dataset is, unfortunately, not public. If I have enough time, I may also test clip on this dataset, and see which one seems to work better (there is no reference genome, but we know the approximate genome size).