Parameters for accurate Oxford Nanopore reads

[jyw-atgithub]

Hi!
What are the best parameters for aligning ONT R10.4 DNA sequences to a genome (Drosophila melanogaster) with highly repeatitive contents? The reads are basecalled by Dorado SUP model v5.2 so the average quality score is 23. Thank you!

[kuanchiun]

Dear Developer,

I also have a similar question.

I’m working with R10.4.1 Dorado-corrected ONT reads and mapping to the human reference genome. I noticed that minimap2 recently added the lr:hq and lr:hqae presets. I tried to approximate the lr:hq settings in winnowmap2 (e.g., -x map-ont -k19 -w19 -U50,500 -g10k), but it appears that winnowmap2 does not provide the -U parameter.

Do you plan to add a preset optimized for R10.4.1 reads in winnowmap2?

If not yet, could you recommend parameter settings for R10.4.1 ONT reads (or the closest equivalent to minimap2’s lr:hq)?

Is there an alternative to -U in winnowmap2, or a suggested combination of options to emulate its effect?

Thank you very much for your time and guidance.

Best regards,
Kuan Chiun