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docs/user-guide/configuration.md

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 # Configuration
+
+## Execution Mode
+
+Accepted values: `patient`, `environment`. Defaults to `patient`.
+
+Defines the execution mode of UnCoVar.
+
+When the mode is set to `patient`, the sample is assumed to be from a single
+host organism and contains only one strain of SARS-CoV-2. The parts of the
+workflow responsible for reconstructing this SARS-CoV-2 strain genome are activated.
+
+If the mode is set to `environment`, the sample is assumed to be from the
+environment (e.g. wastewater) and to contain different SARS-CoV-2 strains.
+The parts of the workflow responsible for creating and analysing individual
+genomes (e.g. assembly, lineage calling via Pangolin) are disabled.