Evaluating and controlling data quality with q2-quality-control

[Nicholas_Bokulich]

Hi @Imee19 ,
This tutorial might be a little clearer, since it shows how to integrate this plugin in a full analysis:

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…

@Imee19

What is the query sequence, is this the output, representative sequences?

the query sequences can be anything you want, but yes this would typically be your representative sequences for your ASVs/OTUs. The query sequences are the input that you want to compare against the reference.

@Imee19

How about the reference sequence, at what step is this generated?

The reference is usually one or more known sequences that you are comparing against. E.g., the exclude-seqs aligns a set of query sequences against the reference sequences to separate hits/misses into different outputs. So you could align against a full reference database (e.g., SILVA 16S sequences) or just a subset of representative sequences to remove non-target DNA (e.g., host genes or others that do not align to the reference).

Good luck!