Non-chimeric reference dataset selection for uchime-ref (reference-based chimera detection) for fungal ITS sequences

[Nicholas_Bokulich]

Hi @Fairytale,

@Fairytale

I’m working on reference-based chimera detecton for fungal ITS sequecne with uchime-ref in QIIME2.

You should download the QIIME release from the page that you linked to. Those sequences will need to be imported into QIIME as described in this tutorial (which also describes how to train a classifier on those sequences if you want to use a naive Bayes classifier on these sequences. You could also download a trained classifier from this tutorial:

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 QII…

@Fairytale

I aware of that it is vsearch plugin in QIIME2 responsible for this analysis

That is incorrect. We do have a taxonomy classification method that uses vsearch for alignment followed by a native LCA algorithm to find consensus taxonomies, but that is in the q2-feature-classifier plugin (along with other taxonomy classifiers), NOT the q2-vsearch plugin.

Good luck!