Using qiime (or mothur) with 16S V1-V3 data

Question

[Nick]

I have Illumina PE reads of 16S V1-V3 data. I've already merged the reads and would like to analyse it using Qiime (or mothur). I assume the standard workflows have to be adapted as they rely on 16S V4 databases. Can anyone suggest a workflow which is specifically adjusted for V1-V3 data?

Answer 1

[Istvan Albert]

If your database contains the full sequence of 16S genes then no changes in the workflow would be needed. See for example

https://mothur.org/wiki/Silva_reference_files