Type Among Multiple Species

The Type among Multiple Species workflow is designed for typing a sample among multiple predefined species (figure 10.10).

Image typemultiplespeciesworkflow
Figure 10.10: Overview of the template Type among Multiple Species workflow.

Similar to the Type a Known Species workflow, it allows identification of the closest matching reference species among the user specified reference list(s), but in this case, the list(s) may represent multiple species. The workflow identifies the associated MLST scheme and type, determines variants found when mapping the sample data against the identified best matching reference, and finds occurring resistance genes if they match genes within the user specified resistance database.

The workflow also automatically associates the analysis results to the user specified Result Metadata Table. For details about searching and quick filtering among the sample metadata and generated analysis result data(see Filtering in Result Metadata Table).