Hi @andrewsanchez, thanks so much for getting back to me! I didn't realize there was a "trunc more to get more" strategy here - thank you for your suggestion. I ended up using (190, 140) as my truncation lengths with a maxEE
of 2 using DADA2 in R per your suggestions, and also used the trimRight
parameter to take off 13 bp off the right side, which would be a useful param to include in qiime2 as well.
I also discovered MultiQC in the interim and noticed a lot of nextera transposae contamination in my sequences, which prompted me to run cutadapt and Trimmomatic (and, subsequently DADA2) outside of qiime, which seems to result in less sequence loss later down the line.
Now to deal with taxonomic classification with COI...hoping someone has a nice pre-trained classifier that can be run locally...one can dream (though shoutout to @devonorourke for the BOLD classifier. Guess it's time to finally learn how to use our servers