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 genes for prokaryotic taxonomic assignment. https://greengenes.secondgenome.com/?prefix=downloads/greengenes_database/
- Silva SSU (16S/18S) and LSU (23S/28S) rRNA for Prokaryotic and Eukaryotic taxonomic assignment. https://www.arb-silva.de/no_cache/download/archive/current/Exports/
- UNITE: ITS spacer for fungal taxonomic assignment. https://unite.ut.ee/repository.php
To run the tool, go to
Toolbox | Microbial Genomics Module (
) | Metagenomics (
) | 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 Update Sequence Attributes in Lists tool (https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Update_Sequence_Attributes_in_Lists.html) 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.