Can Qiime2 moving pictures workflow be used for analyzing variable region V1-V2, including taxonomy?

[zwei (Zhengzheng Wei)]

Can Qiime2 moving pictures workflow be used for analyzing variable region V1-V2, starting from demutiplexed sequencing files?

mostly wondering what trained classifier file to use for taxonomy, [Silva 132 99% OTUs full-length sequences]?

and any other steps need to modify to suit V1-V2 regions,

Thanks a lot,

[ebolyen (Evan Bolyen)]

Hey @zwei,

Yep, really anything that the types let you do should be more or less fine for any amplicon. I think the only thing you should keep in mind is the merging of your reads (if paired) and whether you have enough length in your sequences to make that work.

Otherwise, I believe the Silva full-length classifier should work great. If this is common enough for you, you could also train a classifier specifically on the V1-V2 region, but for any one-off work, the full length is fine.

[zwei (Zhengzheng Wei)]

Thanks, very helpful!