Possible Analysis Pipeline for Ion Torrent 16S Metagenomics Kit Data in QIIME2?

[cjone228 (Carli Jones)]

Thanks for your reply, @Nicholas_Bokulich ! We are still a bit confused at this very section - at first you say "better to stick with vsearch", but then in point 2 you say "the pre-trained full-length 16S classifier would be best". I might just be confused, but I thought these were two separate things. Could you please clarify which we should use? Thank you so much!

@Nicholas_Bokulich

Honestly, it is probably better to stick with vsearch for your case, where there are two issues to overcome for the sklearn classifier:

1. reads in mixed orientations
2. a mixture of primers. It sounds like these effectively cover most of the 16S rRNA gene, so the pre-trained full-length 16S classifier would be your best best. You will not be able to capture the slight accuracy boost that comes from training to the specific primer sites.