Download Custom Microbial Reference Database

The Download Custom Microbial Reference Database tool allows you to create a custom database from taxonomies or NCBI assembly IDs. The tool outputs a single sequence list. It is possible to download the sequence list 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) | Databases (Image databases_folder_closed_16_n_p) | Taxonomic Analyses (Image taxonomic_analysis_folder_closed_16_n_p) | Download Custom Microbial Reference Database (Image create_microbial_reference_database_ncbi_16_n_p)

In the first window (figure 17.3) in the section Customize Database, select one of the three options:

Image downloadcusmirefdb1
Figure 17.3: Select the source of the database

Here you can also choose to skip the database builder. If you choose to skip, all references matching the criteria stated in the next step will be downloaded. Selecting skip database builder will also enable the options to include all annotation tracks (annotation tracks are not needed for taxonomic profiling applications, but required when creating MLST schemes). An additional filter, Minimum contig length, may also be specified. Note that if you have not selected to skip the database builder, these options can be set later when downloading the database.

Click Next to customise the database you wish to generate (as in figure 17.4). You have the following two options:

It is also possible to leave the Linages prefixes and ID matching fields empty. In this case the database will not have any references pre-selected. Selection can then be done manually in the builder.

Image downloadcusmirefdb2
Figure 17.4: Select options for building the database

If Skip Database Builder was enabled, all references matching the specified criteria will be downloaded and the running of the tool is complete and you will not see the Database Builder as described in the next section.