Download Curated Microbial Reference Database

The Download Curated Microbial Reference Database tool downloads selected references as sequence lists and/or taxonomic profiling indexes with the necessary annotations required for the tools in the Typing and Epidemiology and Metagenomics sections of the Microbial Genomics Module.

To run the tool, go to:

        Toolbox | Microbial Genomics Module (Image mgm_folder_closed_flat_16_h_p) | Metagenomics (Image wma_folder_open_flat_16_n_p) | Databases (Image databases_folder_closed_16_n_p) | Taxonomic Analyses (Image taxonomic_analysis_folder_closed_16_n_p) | Download Curated Microbial Reference Database (Image download_curated_microbial_database_16_n_p)

In the first window (figure 15.1), select the database you wish to download.

Image downloadcurmirefdb1
Figure 15.1: Select the database and output format

You can choose between several databases

You can then chose to download the database as an annotated sequence list and/or as a taxonomic profiling index.

The Curated Microbial Reference Databases are optimized for balance in the taxonomic representation across the taxonomy, i.e. the oversampling of some branches of the taxonomy is removed by using representative sequences. This has the consequence that some assemblies may not be particularly good assemblies, yet they are included as they constitute the best current representative of the given branch in the taxonomy. For this optimized database you can choose to download the 22g database, or one that is optimized for running the Taxonomic Profiling tool on a laptop computer with 16GB of main memory. The 16g version of the curated database contain a smaller number of assemblies, in order to be able to run on a system with 16GB of main memory.

Note: some of the databases offered are derived works, licensed under a Creative Commons Attribution-ShareAlike (CC BY-SA) license. We offer free access to those without requiring a CLC product license. They can be downloaded using the CLC Genomics Workbench with the Microbial Genomics Module installed in viewing mode. The downloaded files can then be exported to non-proprietary formats using the freely available viewing mode of the CLC Genomics Workbench.