How to split a folder full of pod5 by phred score?

Question

[compuTE]

Hi,

I'm working on ONT data as pod5 files. Usually, the sequencing device divides the pod5 files in two output folders pod5_pass and pod5_fail. However, this time something failed on that step so I was left with all the reads in a single folder.

I am afraid I'm not very familiar with this file format so I was wondering if anyone has advice on how to split this folder by phred score (10)?

Thanks!

Answer 1

[GenoMax]

Depending on what kind of nanopore device this is it may be simpler for the lab to re-do the basecalling and give you the correct results.

However, this time something failed on that step so I was left with all the reads in a single folder.

So you actually have reads in one of the "fastq_pass"/"fastq_fail" folders or no reads at all. With just POD5 files you can re-do the basecalling (using dorado caller) and then you could use chopper (LINK) to filter the reads to avg quality you need.