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:
- 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 format your own database with your own sequences and a corresponding taxonomy file, use the tool called Create Annotated Sequence List and set the "Taxonomy" field and a Clustering similarity fraction corresponding to the clustering in your sequence list.