Hi @jwdebelius,
Thanks very much @Mehrbod_Estaki for remembering that conversation. I note that the Caporaso primers are still used for the pretrained classifiers. Should we recommend that they update those?
@jwdebelius, there are two options I can think of that won’t take months of development. In my experience they will probably give fairly similar results.
- Just use full length sequences and full length readytowear weights. That is, don’t trim anything.
- Trim your reference db using your V3V4 primers then use it to build new weights for your habitat of choice.
I know you said you were too lazy for the second option, but it is probably just as easy as downloading weights from readytowear. You can probably do it with a single call to clawback assemble-weights-from-Qiita. You would have already done most of the steps in the tutorial.
It’s up to you, though, and it probably won’t make much difference.
I hope that helps.
Ben