Nanopore R9.4 and R9.10

[Aline-Git]

Hello,
Thanks a lot for minimap2, it'a great tool that I use almost every day !

I'm working with ONT sequences. I know that there is a -x map-ont preset specially designed for ONT reads. However, the error rate of ONT reads have continuously decreased since this preset was implemented, thanks to the improvement of basecallers and the new chemistry. The error rate is now less than 5% with the R9.4 chemistry and less than 1% with the chemistry 10.4.

Which options should we use to take these changing error rate into account ?

I tried several combinations, but it does not seem to be optimal.

Thanks,

Aline

[socialhang]

I have a same question