Hi again Colin,
Apologies for the delay. This is a side project and not part of my main research, so I come back to it whenever I have a gap in my schedule.
My idea is to proceed as follows:
1-Get the fastas from the Sanger sequencing (several colonies were tested for each member) and import them into quiime2.
2-With Dada2, generate a set of rep-seqs for each of the strains. This step will also trim the reads to get rid of the primers.
3-Manually introduce the rep-seqs and taxonomy into the database.
4-Using rescript, limit the sequences in the whole database (including the newly manually added rep-seqs) to the Ilumina amplified regions. In my case, I will probably use the NCBI database, as GG is not very updated and SILVA melts the computer. I assume that for this porpoise I can follow the tutorial here.
Is this a good plan to proceed? Might I be missing something?
Kid regards
Jaime