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marbl / Winnowmap

Long read / genome alignment software
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aligning HiFi reads to single pass long reads #23

Open dcopetti opened 2 years ago

dcopetti commented 2 years ago

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 commented 2 years ago

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 commented 2 years ago

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 (https://github.com/lh3/minimap2/issues/801#issuecomment-895619364) - I am thinking about those options as well. Thanks!