Trimming poly-A and poly-T with cutadapt using DADA2

[MatGola]

Hi,
I've been using the example in the following workflow: https://benjjneb.github.io/dada2/ITS_workflow.html

It seems to work just fine so far. I'm trying to understand if there is a way to further use cutadapt to trim poly-A and poly-T
sequences as cutadapt suggests?

Best

[benjjneb]

I think yes, at least according to the cutadapt docs: https://cutadapt.readthedocs.io/en/stable/recipes.html#trim-poly-a-tails

You'll have to look there though for help on cutadapt-specific features.