Set Up Amplicon-Based Reference Database

In addition to the download of reference databases using the Download Amplicon-Based Reference Database tool, you can format your own databases by running the Set Up Amplicon-Based Reference Database tool:

Databases (Image databases_folder_closed_16_n_p) | Amplicon-Based Analysis | Set Up Amplicon-Based Reference Database (Image annotate_otu_taxonomy_16_n_p).

This tool takes as input QIIME-format fasta files (typically clustered into OTUs at 99, 97, 94, and 90 percent similarity) and corresponding taxonomy mapping files, where each line of the taxonomy file contains an OTU name and its taxonomy. The OTU name and its taxonomy must be separated by a tab character while taxonomy levels are separated with semicolons. For example, the following line

o123 k__Bacteria;p__Bacteroidetes;c__Sphingobacteria;o__;f__;g__;s__.

indicates that the OTU o123 belongs to the class Sphingobacteria and that its taxonomy is specified only up to the class level. For more information about QIIME format, see