Map non noisy ONT

Hello,

I have a question: according to Oxford nanopore their last cells produce very accurate reads. Does "map-ont" still work as the best setting to map those reads? I am asking because the manual still refers to "long noisy reads". Thanks for minimap2 and for your time.

Sorry I hadn't seen issue

#1030 (comment)

So, I understand that Dorado is accounted for now in the map-ont settings?

Thanks for all the work you are doing.
Alex

[iiSeymour]

@Axze-rgb dorado aligner has not yet changed any of the index settings and when we do we would like them upstreamed here.

[lh3]

For now, use map-ont. You can try -x map-hifi -w10 (HiFi scoring and k-mer length with more seeds) for Q20 reads but you need to have a way to evaluate whether that gives better results.

I hope I can find some time in the next several months to improve minimap2 a little bit. Along this I will be testing alternative scoring for v14 data.

[lh3]

@iiSeymour When you find more appropriate parameters for aligning Q20 reads, I will be happy to add a new preset for that. This will also save me some time. Thanks!

[Checunmily]

For now, use map-ont. You can try -x map-hifi -w10 (HiFi scoring and k-mer length with more seeds) for Q20 reads but you need to have a way to evaluate whether that gives better results.

I hope I can find some time in the next several months to improve minimap2 a little bit. Along this I will be testing alternative scoring for v14 data.

hello, recently I've been dealing with some R10 data and I want to know if there are any plans to make some improvements of minimap2 on ONT R10 in the next few months? Or any new suggestions for R10 data?

[iiSeymour]

@lh3 from our internal benchmarking we find speed and downstream accuracy are maximized with -x map-ont -k19 -w 19 -U50,500 -g10k.

[Mon3trK]

For now, use map-ont. You can try -x map-hifi -w10 (HiFi scoring and k-mer length with more seeds) for Q20 reads but you need to have a way to evaluate whether that gives better results.

I hope I can find some time in the next several months to improve minimap2 a little bit. Along this I will be testing alternative scoring for v14 data.

Hi @lh3, accuracy of ONT sequencing has advanced a lot from duplex or R10.4 pore. I also wonder if there is any plan for setting different preset for R9 and R10 nanopore? And also different basecallers have significant impact on sequencing accuracy, it seem unappropriate to just mixed in -x map-ont.

[lh3]

from our internal benchmarking we find speed and downstream accuracy are maximized with -x map-ont -k19 -w 19 -U50,500 -g10k.

-x map-hifi is equivalent to -x map-ont -k19 -w 19 -U50,500 -g10k -A1 -B4 -O6,26 -E2,1 -s200. The main difference here is the scoring. How scoring affects the downstream tools? If the map-hifi scoring also works, I can add an alias to map-hifi, something like lr:hq.

also different basecallers have significant impact on sequencing accuracy

That is why it is more appropriate to choose a conservative setting that can give you good results on input of varying quality.

[iiSeymour]

If the map-hifi scoring also works

Unfortunately not, the map-hifi scoring leads to both fewer mapped reads (~3%) and small regressions in SNP/INDEL calling. It's possible these regressions could be recovered from new models trained on updated scoring parameters but it seems -x map-ont -k19 -w 19 -U50,500 -g10k is the sweet spot.

[lh3]

The next release will have a lr:hq preset for -k19 -w 19 -U50,500 -g10k.

[bepoli]

Thanks @lh3 !
I understand that the new preset lr:hq is not meant for spliced alignment.
Should I use the existing preset splice:hq with highly accurate Nanopore cDNA reads? (with average quality >= 20)