Typing samples of a single known species
The Type a Known Species workflow is designed for typing of samples representing a single known species (figure 8.1). 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.
Figure 8.1: Overview of the template Type a Known Species workflow.
Subsections
- Preliminary steps to run the "Type a Known Species" workflow
- How to run the "Type a Known Species" workflow for a single sample
- Example of results obtained using the Type a Known Species workflow
- How to run the "Type a Known Species" workflow on a batch of samples: