Type a Known Species (legacy)

Note this is the legacy version of the workflow found in section Type a Known Species. We recommend avoiding using legacy workflows when possible. If you find missing functionality, please get in touch at [email protected]

The Type a Known Species (legacy) workflow is designed for typing of samples representing a single known species (figure 24.44). 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.

Image legacy_typeknownspeciesworkflow
Figure 24.44: Overview of the template Type a Known Species (legacy) workflow.