Option to handle read-through into primer for its sequences

[paulzierep]

We want to use lotus2 to analyze ITS sequences. A common issue is the read-through into the opposite primer as described in the dada2 toturial: https://benjjneb.github.io/dada2/ITS_workflow.html Can lotus trim primers in such cases. I could not find it in the docs. Alternatively one could use cutadapt and then use lotus2 on the trimmed reads I guess... We will develop a toturial for such as case in Galaxy and I wanted to check what would be the best approach from your point of view ?