Hello, Will the pipeline remove the primer sequences and anything that comes before (F primer) or after them (R primer), like adaptor sequences? The pipeline clearly states that only the primer sequence should be included in the code. Do I need to remove adaptor sequences prior to launching the pipeline? Thank you!

Hi.

Will the pipeline remove the primer sequences and anything that comes before (F primer) or after them (R primer), like adaptor sequences?

Yes

Do I need to remove adaptor sequences prior to launching the pipeline?

No

The pipeline clearly states that only the primer sequence should be included in the code

Yes, because under certain settings the primers are also used to extract sequences from the reference taxonomy database. And here adapter sequences are very problematic.

Wonderful. Thank you very much!