Add NGS MLST Report to Scheme

Once the MLST typing has been performed, and new types have been identified, it is possible to use the generated Consensus NGS MLST Report as input for the Add NGS MLST Report to Scheme tool and hereby add new typing information to an existing MLST scheme.

        Databases (Image databases_folder_closed_16_n_p) | NGS-MLST (Image mlst_folder_closed_16_h_p) | Add NGS MLST Report to Scheme (Image add_sequences_to_scheme_16_h_p)

Specify the report output file(s) of the Identify MLST tool to be used (figure 17.5).

Image addmlst_toscheme1
Figure 17.5: Input files are Consensus NGS MLST Reports.

Then select the scheme you would like to add the newly found MLST type(s) to (figure 17.6). This scheme should have the same genes listed than in the report(s) specified in the first step. Any report that have a mention "Not found" for the status and allelic profile will be considered as incompatible with a scheme. A warning is issued in the dialog and the tool cannot be started.

Image addmlst_toscheme2
Figure 17.6: Select the relevant MLST scheme for adding the reported MLST type.

Save the updated scheme in the folder where you have stored database and downloaded schemes.