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polio-nanopore / piranha

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Rapid barcoding kit #225

Closed a-qvecell closed 3 months ago

a-qvecell commented 3 months ago

Hello, Is it possible to run PIRANHA using the Rapid Barcoding Kit? From the customise_run.py file, it looks like it might be possible, and maybe it is just a matter of lowering the minimum read length - but maybe there are other things to be aware of. Can you enlighten me here? :)

Best, Amanda

PS In the README, two different default min percentages are mentioned - 2% and 10%. From what I can see from the --help text, 10 should be the default :)

aineniamh commented 3 months ago

Hi Amanda! There shouldn't be any reason it wouldn't work with the rapid barcoding kit- I guess if the read lengths are much shorter there might be coverage issues along the VP1 region (i.e. if it's not fully amplified)- or are you doing whole genome sequencing? I'm working on a PR at the moment that will include a depth masking for incompletely mapping reads (with divergent wt polio sequences in mind) that will handle that, but I haven't quite got it ready to merge yet!

a-qvecell commented 3 months ago

Ok, thank you :)