Yacht usage article

[mfl15]

No description provided.

[xiangchaoyuan1027]

Is YACHT applicable to ONT reads?

[dkoslicki]

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]

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! — Reply to this email directly, view it on GitHub, or unsubscribe. You are receiving this because you commented.Message ID: ***@***.***>