Heterogeneity Spacers and Primers

Hi @marcelm,

thank you for the development of Cutadapt.
I'm actually using the latest stable version and python 3.10.

I'm dealing with these heterogeneity spacers+primers:

Bacterial region V3-V4:
341F (5´-CCTACGGGNGGCWGCAG-3´)
341Fb (5´-TCCTACGGGNGGCWGCAG-3´)
341Fc (5´-ATCCTACGGGNGGCWGCAG-3´)
341Fd (5´-TGTCCTACGGGNGGCWGCAG-3´)
785R (5´-GACTACHVGGGTATCTAATCC-3´)

I would like to know if you know a suggested way to deal with that.
I was thinking to use a file in which I insert these primers (like demultiplexing) but the problem is that basically they are representing the same primers, all equally used on same samples, so I dont need to have 4 different output for each and if I set the files like:

341F
...
341Fb
...
...I feel that this, of course, will lead to different outputs based on the type of primer sequences given, so I'm pretty sure that this is not the right approach.

Do you have suggestions?

The issue does not name any files, tests, or entry points. Start by reviewing Cutadapt's primer and adapter matching behavior and its demultiplexing documentation, then determine whether equivalent primer variants can be handled as one trimming target without separate outputs; done would be a documented supported approach.