Hi, our organisms have diagnostic information within a variable primer region which may have 0-5 mismatches. We need to trim our sequences but keep the primers with an option that allows x number of mismatches within the primer sequence. It would be AWESOME if Mothur could do this.
Mothur already has this option. The keepforward parameter allows you to indicate whether you want the forward primer removed or not. The default is F, meaning remove the forward primer.