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

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?

sequencing
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written by O.rka O.rka

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

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written by medelin.ocejo • medelin.ocejo

1 answer

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

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written by O.rka O.rka

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