Hi,
to remove the 5’ primer (--p-front) and the 3’ primer (--pp-adapter) simultaneously, applying --p-times 2 worked excellent!
As you mentioned, cutadapt has the interesting linked-primers feature. According to the docs, this trims primers only, if the 5’ forward AND the 3’ reverse primers are matching. This feature is not mentioned in the qiime 2 cutadapt docs. Is it already possible to use the cutadapt linked-primer feature in qiime2, or do I have to use cutadapt “stand alone” (which, of course, does not except qiime2 artifacts).
In the cutadpt docs, I also found that a --discard-untrimmed feature (or --untrimmed-output FILE) is implemented, allowing to remove sequences without matching adapters (besides only trimming off matching adapters). Is it planned to make this feature also available for qiime2?
Best,
Martin