Recipes

Welcome to our cookbook, where complex bioinformatics processes are simplified into easy-to-follow steps! Just like a recipe in cooking breaks down a gourmet dish into manageable ingredients and instructions, our ‘Recipes’ transform complex genomic analyses into straightforward pipelines. Here, we offer a collection of curated workflows, or ‘recipes’, each designed to tackle specific bioinformatic questions using the AQuA-tools suite of 3D genomics tools.

To get started with AQuA-tools, you can download the toolkit from our GitHub repository. Installation instructions for both local and container-based environments are provided there.

Recipes for Local Environments

Recipe 00: Assessing differences in interactions between peaks

Recipes for Docker/Tinker Environments

Recipe 01: Calling loops from a sample

Recipe 02: Creating meaningful subsets

Recipe 03: Making sense of loop networks