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

[Ge0rges]

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.

[mikolmogorov]

Thank you - I'll give it a test!

[Ge0rges]

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

[mikolmogorov]

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

[Ge0rges]

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.

[mp15]

Might I suggest we experiment with lr:hqae from 2.28+ and dropping the -k 18? That preset was designed to map ONT Q20 long reads back to their assembly.