Forward and Reverse primer removal

Hi @Brigitta1,

No, qiime2 does not automatically remove the primers, it is agnostic of the primer used in your experiment!
For this, you can use the q2-cutadapt plug in:

https://docs.qiime2.org/2022.2/plugins/available/cutadapt/trim-single/

I usually use this as first step, to avoid possible problems at denoising stage. However, anytime before taxonomy assignation step should do!

Hope it helps
Luca

2 Likes