I looked at the tutorial and links you sent. I want to use the open reference option but I imagine I need to first train the reference database (SILVA 99%). I downloaded the lastest version of QIIME compatible ones from here. I unzipped the file and am looking at the taxonomy files and the sequences. There are many different ones. I imagine for the sequence, I need to get the rep-set-aligned 99%, the one that is called 99_alignment.fna.zip. For the taxonomy file, should I use the one from the 16s folder that is called consensus_taxonomy_all_levels? There are raw-taxonomy and other files too.
