Download Amplicon-Based Reference Database
Amplicon-based reference databases contain a list of representative amplicon sequences and their taxonomy. Databases like these are 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. The database is available in three differently clustered versions, 97% similarity, 99% similarity, and dynamic, in which sequences are dynamically clustered at similarities between 97-99%. Additionally, each of these three databases are available in a version with and without singletons. Singletons are fungal taxons for which only one ITS sequence is available [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/).
- RefSeq Prokaryotic 16S. 16S ribosomal RNA sequences from bacteria and archaea. The sequences are curated by the NCBI RefSeq Targeted Loci Project (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/).
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.