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.

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)

Under Customize Database, select whether to include genomic and/or plasmid sequences (figure 15.3):

Image downloadcusmirefdb1
Figure 15.3: Select type of sequences to include and whether to skip the Database Builder.

Choose whether you wish to skip manual selection:

Click Next to customize the database (figure 15.4):

Image downloadcusmirefdb2
Figure 15.4: Specify accession or TaxIDs, or taxonomic lineages to include in the database.

Click Finish.

If Skip Database Builder was selected, all genomes matching the specified criteria will now be downloaded. If the enabled ID or Taxonomy matching field was left empty, no genomes will be downloaded.

If Skip Database Builder was left unchecked, a reference database is not downloaded right away. Instead, the Database Builder will open, see Database Builder.