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:
- SILVA: SSU (16S/18S) and LSU (23S/28S) rRNA sequences for Prokaryotic and Eukaryotic taxonomic assignment. https://www.arb-silva.de/no_cache/download/archive/current/Exports/
- MiDAS: 16S rRNA sequences for Prokaryotic and Eukaryotic taxonomic assignment of microbes in wastewater treatment and bioenergy systems. https://www.nature.com/articles/s41467-022-29438-7
- UNITE: ITS sequences for fungal taxonomic assignment. https://unite.ut.ee/repository.php
- Greengenes: 16S rRNA sequences for prokaryotic taxonomic assignment. https://greengenes.secondgenome.com/?prefix=downloads/greengenes_database/
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.