aligning HiFi reads to single pass long reads

[dcopetti]

Hello,

I would like to align PacBio HiFi reads to ONT reads with the goal of making a consensus of the alignment against the long read backbone (to correct the errors).
First, I wonder whether Winnowmap is suitable for that, or if I should use minimap2 instead.

Then, in this case the reference is of lower quality (median Q score 11) and the query has much higher accuracy (Q 31): will this affect the choice of the alignment parameters? Can I use -x map-ont or asm20 as presets?

Lastly, I have more than 200 Gb of raw ONT reads that I would like to error correct with ~60 Gb HiFi data: I thought of splitting the "reference" to have small jobs and shorter time to compute the index. Is this a good approach or will splitting affect the representativeness of the minimizers?

Thanks,
Dario

[cjain7]

This may not be a good use-case for Winnowmap. map-ont or asm20 presets are designed to map reads to a reference/assembly in both Winnowmap and minimap2. Each read is expected to have a single primary mapping.
Maybe you can write to minimap2 authors to see if minimap2 would allow this, and using what preset. I'd assume presets for read overlapping may work better.

[dcopetti]

Good point: it looks more like a all-vs-all rather than a read-to-reference type of exercise.

Heng Li advised me to map ONT reads to unitigs, which is another strategy as well (lh3/minimap2#801 (comment)) - I am thinking about those options as well.
Thanks!