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kapsakcj committed Nov 8, 2024
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5 changes: 3 additions & 2 deletions docs/workflows/standalone/dorado_basecalling.md
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Expand Up @@ -12,17 +12,18 @@ The Dorado Basecalling workflow is used to convert Oxford Nanopore `POD5` sequen

### Model Type Selection

Users can configure the basecalling model by setting the dorado_model input parameter:
Users can configure the basecalling model by setting the `dorado_model` input parameter:

Default Model: "sup" (super accuracy) is used unless overridden by the user.
Manual Model Input: Users can specify the full path or name of a specific model (e.g., [email protected]).
Automatic Detection: When set to sup, hac, or fast, Dorado will automatically select the appropriate model version if available.

- **Model Type (sup):** (super accuracy) The most accurate model, recommended for critical applications requiring the highest basecall accuracy. It is the slowest of the three model types.
- **Model Type (sup):** (Super Accuracy) The most accurate model, recommended for critical applications requiring the highest basecall accuracy. It is the slowest of the three model types.
- **Model Type (hac):** (High Accuracy) A balance between speed and accuracy, recommended for most users. Provides accurate results faster than `sup` but less accurate than `sup`.
- **Model Type (fast):** (Fast Model) The fastest model, recommended when speed is prioritized over accuracy, such as for initial analyses or non-critical applications.

### Example Manual Models:

- `[email protected]`
- `[email protected]`
- `[email protected]`
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