Create MLST Scheme with Sequence Types

The Create MLST Scheme with Sequence Types workflow creates a MLST scheme from references and adds sequence types by typing references and adding the results to the scheme.

To run the Create MLST Scheme with Sequence Types workflow, go to

        Toolbox | Template Workflows (Image workflow_group) | Microbial Workflows (Image mgm_folder_closed_flat_16_h_p) | Typing and Epidemiology (Image typing_epi_folder_closed_16_h_p) | Create MLST Scheme with Sequence Types (Image create_large_mlst_wf_16_h_p)

You can select one or more assemblies as input (figure 13.36). At least one of the assemblies must be annotated with CDS regions.

Image mlst_wf_input
Figure 13.36: Select the high-quality references serving as the basis for the scheme

In "Create MLST scheme" dialog (figure 13.37), the settings for the scheme creation can be viewed and changed.

Image mlst_wf_create_scheme
Figure 13.37: Parameters for creating the initial scheme

The parameters that can be set are:

In "Add Typing Results to MLST scheme" dialog (figure 13.38), sequence types will be added to the scheme. In addition, the following parameters can be specified:

Image mlst_wf_add_types
Figure 13.38: Add Typing Results settings

In the Result handling window, pressing the button Preview All Parameters allows you to preview - but not change - all parameters. Saving the output will generate the files shown in (figure 13.39) and optionally, a workflow result metadata table.

Image lmlst_wf_output
Figure 13.39: The output from Create MLST Scheme with Sequence Types

For more information on the tools and MLST schemes, see