Flye Update minimap2 to v2.27 and use faster HQ ONT alignment

Minimap2 v2.27 was released a couple days ago and includes a new significantly faster alignment preset lr:hq for Q20 nanopore reads. Here I update minimap2's version and make use of that preset in the map-ont mode.

Mar 14 '24 23:03 Ge0rges

Thank you - I'll give it a test!

Mar 15 '24 12:03 mikolmogorov

Hi @mikolmogorov I was wondering if you've had a chance to build this in?

Aug 05 '24 21:08 Ge0rges

hi @Ge0rges

Did you try to compare the flye performance before/after the update on a Q20 data? What's the performance gain? Flye already had specialized minimap2 parameters for --nano-hq

Aug 06 '24 12:08 mikolmogorov

Hi @mikolmogorov I did benchmark this a while ago and if I recall correctly see a slight improvement on my data however it is a mean Q12 despite using the new chemistry. I haven't tried on proper Q20 data. Unsure whether the accuracy impacts the unalignment significantly either.

Aug 06 '24 15:08 Ge0rges