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:
- Greengenes: 16S rRNA gene from ribosomal Small Subunit for Prokaryotic taxonomic assignment clustered OTUs at different percentages. http://greengenes.secondgenome.com/downloads
- Silva/Arb SSU: 16S/18S rRNA from ribosomal Small Subunit for Prokaryotic and Eukaryotic taxonomic assignment clustered OTUs at different percentages. http://www.arb-silva.de/download/archive/qiime/
- UNITE: ITS spacer clustered OTUs at different percentages for fungal taxonomic assignment. https://unite.ut.ee/repository.php
To run the tool, go to
Databases () | Amplicon-Based Analysis | Download Amplicon-Based Reference Database ().
Select the database needed and specify where to save it. When using this tool, the databases downloaded are automatically formatted.
If you wish to look at the databases in a table format, you can see that only the columns Name, Size and Start of Sequence are populated, leaving the column about taxonomy empty. That is because taxonomy for each sequence is embedded in the sequence object used to create OTUs, while it will not appear in the database tables. As none of the tools will ever use the information present in the "Taxonomy" column from these tables, it is irrelevant to try to add or edit the names in them yourself.
If you wish to format your own database with your own QIIME formatted sequence and a corresponding taxonomy file, use the tool called Set Up Amplicon-Based Reference Database.