Examples of databases
Databases can be readily created for the Create Taxomic Profiling Index and OTU Clustering tools. This only requires specifying a Taxonomy metadata annotation on the sequences, and optionally, for OTU Clustering, specifying a clustering similarity fraction.
Notice, in earlier version of the Microbial Genomics Module, the Set Up Microbial Reference Database and Set Up Amplicon-Based Reference Database tools were used to create these kinds of databases.
To create a database which can be used together with the Find Resistance using Nucleotide DB tool, several combinations of metadata are possible. Some examples:
- To create a database similar to the QIAGEN Microbial Insight - Antimicrobial Resistance database, the following columns should be present: "Phenotype", "Compound class", and "Gene ARO".
- To create a database similar to the VFDB Nucleotide Database, the following columns should be present: "Virulence factor", "Virulence factor ID", "Virulence gene", and "Virulence gene ID".
It is recommended to use the column names from an existing database (e.g. one obtained using Download Resistance Databases) as a template for new databases. This ensures the metadata is correct and consistent.