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LooseLab / readfish

CLI tool for flexible and fast adaptive sampling on ONT sequencers
https://looselab.github.io/readfish/
GNU General Public License v3.0
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R10/Q20+ #163

Closed daniel007s closed 2 years ago

daniel007s commented 2 years ago

Hi, I was wondering if there's any technical/hard-coded reason why an R10 flow cell with Q20+ prep wouldn't be compatible with readfish? I have yet to try but would like to.

Many thanks,

Daniel

nathanconr commented 2 years ago

Anything on this? So far all I have seen are examples of R9 compatibility but I would like to try this with R10. Thanks, Nathan

mattloose commented 2 years ago

So - this is perhaps one for @alexomics to comment on - we did see some issues on R10 with how we were implementing readfish but we believe these now to be resolved. I would suggest if you are just using a simple static panel to try ONT's built in adaptive sampling. If you want to do something more sophisticated (e.g barcodes with different panels etc) then you would need to use a specific branch to better handle the mux scans (this appears to be especially an issue with kit14).

nathanconr commented 2 years ago

Thank you for the quick answer! What I would like to do is have a single target panel on all barcodes (R10 flow cell with kit14 library). I guess the built in adaptive sampling would be the option of choice then.

mattloose commented 2 years ago

Yes - I'd try that. We would be interested in knowing how it performs...

nathanconr commented 2 years ago

I will keep you updated!