hello,
Im fairly sure this can be done but not sure whats best strategy. How can one eliminate ASVs that correspond to specific taxa from the ASV file generated by DADA2. So one gets the taxonomy assignment, identifies the taxa. Target taxa can be filtered out from the sequence table but not from original ASVs, because those dont have taxonomy assigned. One can identify the actual ASVs corresponding to target taxa, but what tool can be used to apply a filter to the master ASV file (repseqs)? I cant find that one...
I understand you already filtered your feature table with qiime taxa filter-table. I think now you are looking for qiime taxa filter-seqs in order to filter your representative sequences file.