Download Amplicon-Based Reference Database
Amplicon-based reference databases contain a list of representative amplicon sequences and their taxonomy. Such database is required for amplicon-based analysis (Amplicon-Based Analysis).
The following databases are available:
- SILVA. Small subunit (SSU; 16S/18S) and large subunit (LSU; 23S/28S) ribosomal RNA sequences for prokaryotic and eukaryotic taxonomic assignment [Quast et al., 2012] (https://www.arb-silva.de/no_cache/download/archive/current/Exports/).
- MiDAS. 16S ribosomal RNA sequences for prokaryotic and eukaryotic taxonomic assignment of microbes in wastewater treatment and bioenergy systems [Dueholm et al., 2022] (https://www.midasfieldguide.org/guide/downloads).
- UNITE. Internal transcribed spacer (ITS) sequences for fungal taxonomic assignment [Kõljalg et al., 2020] (https://unite.ut.ee/repository.php).
- Greengenes2. Full length 16S ribosomal RNA sequences from the backbone of the Greengenes2 phylogenetic tree. For prokaryotic taxonomic assignment [McDonald et al., 2022] (https://greengenes2.ucsd.edu/).
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.