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The Freyja cookbook

Here, we provide example workflows for doing wastewater analysis with Freyja, using both the command line as well as the Terra computing ecosystem.

Contents:

1. Command Line Workflow
2. Terra Workflow
3. Custom plotting tutorial
4. Barcode analysis tutorial
5. Mutation co-occurrence analysis tutorial
6. Cryptic variant detection tutorial

Let us know if there's anything else you'd like to see!