Download Amplicon-Based Reference Database

OTU reference databases contain representative OTU sequences and their taxonomy. They are needed to perform reference-based OTU clustering. Three popular reference OTU databases, clustered at various similarity percentages, can be downloaded using the Download Amplicon-Based Reference Database tool:

All of the above databases are available at different clustering levels of sequence similarities.

To run the tool, go to

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Databases (Image databases_folder_closed_16_n_p) | Amplicon-Based Analysis (Image otutools_open_16_n_p) | Download Amplicon-Based Reference Database (Image download_otu_refdb_16_n_p)

Select the database needed and specify where to save it. When using this tool, the databases downloaded are automatically formatted.

If you wish to format your own database with your own sequences and a corresponding taxonomy file, use the Update Sequence Attributes in Lists tool ( to set the "Taxonomy" field. A clustering level for such custom databases can not be set on the data object directly, but it may be specified as a parameter when running the OTU Clustering tool.