Will Nanopore-related tools be updated to accept pod5 files?

I’d like to use some of the tools designed to accept nanopore data. My data are in pod5 format, and the tools (Nanopolish Variants, specifically) only accept the fast5 format. Are there plans to update the tools to accept pod5 files? I tried to load a pod5 file as a substitute for the fast5, but got an error. Thanks.

Hi @lkothera

Not that I know of, and it seems that Oxford Nanopore is recommending that users store the read data itself in a fastq format for compatibility reasons.

And, it seems the underlying tool hasn’t been updated to accept alternative formats either. You could ask them about potential updates. If the underlying tool updates, then changes in Galaxy would be much more likely, too.

What to do: Try converting your data first to a format that Galaxy works with (and that the tools in Galaxy work with), then Upload for downstream analysis.

Others are welcome to add more updates to this :slight_smile:

Thanks for this info. I can have the data in fastq format. I’ll see about messaging the tool developers too.

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