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KoslickiLab / YACHT

A mathematically characterized hypothesis test for organism presence/absence in a metagenome
MIT License
28 stars 7 forks source link

Yacht usage article #113

Open mfl15 opened 6 months ago

xiangchaoyuan1027 commented 1 month ago

Is YACHT applicable to ONT reads?

dkoslicki commented 1 month ago

We did not test it on ONT reads, but there is nothing technical stopping YACHT from at least running on ONT reads. My concerns would be 1: ONT reads have a different error profile that can more severely violate the point mutation assumption and 2: YACHT is meant (by default) to work with large (read: Illumina) sequencing sets. For smaller ones, you could decrease the scale factor (eg. scale = 10), but would need to be sure your training database matches. If you have a benchmark/ground-truth ONT data set, we'd definitely be interested in hearing what you find!

xiangchaoyuan1027 commented 3 weeks ago

Thanks a lot

---- Replied Message ---- | From | David @.> | | Date | 07/12/2024 00:02 | | To | KoslickiLab/YACHT @.> | | Cc | xiangchaoyuan1027 @.>, Comment @.> | | Subject | Re: [KoslickiLab/YACHT] Yacht usage article (Issue #113) |

We did not test it on ONT reads, but there is nothing technical stopping YACHT from at least running on ONT reads. My concerns would be 1: ONT reads have a different error profile that can more severely violate the point mutation assumption and 2: YACHT is meant (by default) to work with large (read: Illumina) sequencing sets. For smaller ones, you could decrease the scale factor (eg. scale = 10), but would need to be sure your training database matches. If you have a benchmark/ground-truth ONT data set, we'd definitely be interested in hearing what you find!

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