Hi Mike,
Yes, the database was edited. We first removed one sequence that was an exact replicate of another sequence. I wrote about that on the QIIME Forum as well as the GTDB forum. We then removed 56 more ASVs that we found to be misannotated based on our isolates data and also based on blast results. The script that I used to generate the database is here:-
GtDB_Classifier_Script.txt (3.3 KB)
Do you think this process that we undertook is wrong? Thank you so much for looking into this.
Ankur