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aligning HiFi reads to single pass long reads #23
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This may not be a good use-case for Winnowmap. |
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. |
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
orasm20
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
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