ipyrad2 Documentation

This site is the user guide and command reference for ipyrad2. It covers installation, files and data types, assembly workflows, output exports, task-focused recipes, and downstream analyses.

Start Here

If you are new to the project, begin with What Is ipyrad2?. It provides the project overview and directs you to the most useful next steps.

Find What You Need

• Installation — install ipyrad2 and verify your environment.
• Files and Data Types — understand supported inputs, outputs, and workflow entry points.
• Assembly Quick Guide — follow the assembly workflow from input data to assembled outputs.
• Writing Outputs — filter and export data for external tools.
• Recipes — find focused examples for specific tasks.
• Analysis Guide — choose and run downstream analyses.