What is the recommended way to subsample Oxford Nanopore (ONT) fastq reads with matching fast5?

Question

[O.rka]

I want to run nanopolish and I have some large fastq files. I want to subsample them but I also need the fast5 for the subsampled reads. What is the best method to do this considering the size distributions of the ONT reads?

[medelin.ocejo]

Hi O.rka, did you manage to find the best way to downsample your dataset?

Answer 1

[O.rka]

I didn’t end up doing it but check out this thread. There is a tool that is recommended: https://github.com/nanoporetech/ont_fast5_api/issues/36