Workflows

AQuA-Tools offers two types of workflows to support different stages of your analysis:

📄 Code Snippets are short, focused scripts that show how to use AQuA-Tools for specific tasks, such as calling, visualizing, or intersecting loops. They are designed to be quick to run and easy to follow, and can be used as-is in both Tinker and Docker environments. Snippets are ideal for testing out individual tools and learning how they work.

🧬 Biological Recipes are more robust and realistic workflows that guide users through complete analyses focused on answering biological questions, such as “is there a global observable difference in interaction counts between the interaction spaces of peaks between treatment and control?” Each recipe contains instructions for setting up a working environment, a motivation section that describes the biological question, an analysis pipeline that combines multiple tools, and a conclusion section that interprets the results. Recipes are ideal for users who want to apply AQuA-Tools to complex analysis scenarios or better understand the biological context behind the tools.

To get started with AQuA-tools, visit our GitHub repository.