Download Pathogen Reference Database

Download a collection of bacterial assemblies and enrich with metadata from the NCBI Pathogen Detection Project (see

        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 Pathogen Reference Database (Image download_bacteria_ncbi_16_h_p)

This will open the following wizard window (figure 17.7):

Image ncbi_downl_settings
Figure 17.7: Downloading assemblies and metadata for a selected pathogen from the NCBI Pathogen Detection Project.

The settings are:

Specify a location to save the database. We recommend to create a folder where you can save all the databases and MLST schemes necessary to run some of the CLC Microbial Genomics Module tools.

The resulting database includes a list of different bacterial genome sequences as well as the associated accession numbers, descriptions, taxonomy and size of the sequences. In addition, each reference genome will be annotated with the following metadata (when available):

Once a database has been downloaded, it is possible to extract a subset following the instructions described in Extracting a subset of a database.