Andrea Spitaleri

> ah. ok. the coverage from mosdepth is 26% less than from qualimap. > I don't know how qualimap works, but you could try running mosdepth with --fast-mode and see...

Hi basically I have a bundle of fast5 files from a MinIon run which includes sequencing from different bacterial strains (i.e. samples). Normally, I do basecall and then demultiplex using...

Right. So there is not possibility to avoid to go through basecalling/demultiplexing first, without using fastq files. Actually MinIon makes a sequencing_summary.txt during the run when generating fast5 only. Could...

So the approach described here https://psy-fer.github.io/SquiggleKitDocs/MotifSeq/#background in the Nanopore adapter identification is not useful for this.

Well, my purpose is to bypass the basecalling in order to reduce one source of error and then use uncalled pipeline (https://github.com/skovaka/UNCALLED) to map fast5 on genome reference, i.s. amplicon...

The idea is to run it after run on amplicons so on huge depth (>4000), and then compare with standard procedure to check whether the approach is feasible of course....

Let me see if I understood well. Basecall/demultiplex the fast5 using i.e. guppy. Then as you suggested https://github.com/Psy-Fer/SquiggleKit/issues/46#issuecomment-797118955 get the fast5 per barcode using the sequencing_summary and then use the...

Yep! I will update you how it does. In case it is better, we need then to think how to avoid the step of basecalling ... but this in another...

Uaooo - that sounds great really. Keep in touch then!

I see indeed that you have similar but for RNA https://github.com/Psy-Fer/deeplexicon. Good to know