Type a Known Species

The Type a Known Species workflow is designed for typing of samples representing a single known species (figure 12.33). It allows identification of the closest matching reference species among the user specified reference sequences, identifies the associated MLST, 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.

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Figure 12.33: Overview of the template Type a Known Species workflow.