ITS2 analysis SOP with QIIME 2?

[Nicholas_Bokulich]

Welcome to the forum @Bridget_Makhahlela !

I recommend looking at the "tutorials" section of this forum for some relevant materials. E.g., there is a tutorial for the q2-itsxpress plugin, as well as this tutorial that describes some more steps in a typical ITS analysis workflow:

Fungal ITS analysis tutorial

Fungal ITS analysis, mock communities, and more fun NOTE: This tutorial was written in a QIIME 2 2018.11 environment. It is not guaranteed to work with earlier or later versions of QIIME 2. This tutorial was compiled as a working exercise for a QIIME 2 workshop in December 2018, and does not represent the only possible fungal ITS workflow with QIIME 2, or even a benchmarked protocol recommendation. See other tutorials, e.g., the q2-itsxpress tutorial for other fungal ITS analysis options in QI…

Please check those out and open a new topic if you run into any more questions.

good luck!