Mycobiome_ITS_Remove primers & barcode sequence

[pmehta (pooja)]

Hello everyone,

I have a data set for targeted sequencing (ITS). So far, I have completed my steps for importing the data, summarizing and visualizing it. Before proceeding with DADA2 I want to remove the barcode and primer sequences. The primers are ITS5 & ITS2.

After going through the forum posts I am a bit confused about the best way to do this.
What is the best approach if I have multiple barcode sequences to remove?

I will be very thankful if anyone can guide me in this.

I have attached my metadata file for your reference.METADATA.tsv (1.7 KB)

[Nicholas_Bokulich]

You can use q2-cutadapt for this. See this tutorial for an example with fungal ITS data:

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…