AQuA Tools: clear and reliable BEDPE operations for 3D genomics

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• The genome interacts within the cell nucleus, mediating crucial processes like gene regulation and cell identity.
• Identifying therapeutic targets from non-coding variants requires accurate assignment of variants to genes via 3D genome interactions.
• Current bioinformatics tools for 3D genomics, such as those analyzing HiC and HiChIP data, are cumbersome and not designed for 3D data structures like contact matrices and BEDPE files.

Purpose of the Study:

• To develop a new suite of bioinformatics tools specifically designed for 3D genomics data analysis.
• To provide researchers with intuitive, reliable, and versatile command-line tools for processing contact matrices and BEDPE files.
• To facilitate the integration of 3D genomic data into research for population genetics, cancer research, and precision medicine.

Main Methods:

• Development of AQuA Tools, a collection of shell- and R-based command-line utilities.
• Implementation of core operations tailored for contact matrices and BEDPE files.
• Enabling chaining of core operations with standard UNIX commands for flexible analysis.

Main Results:

• AQuA Tools offers a set of core operations for 3D genomics data analysis.
• The tools are designed to be clear, reliable, intuitive, and versatile for various research applications.
• AQuA Tools aims to be accessible for novice users while serving as a powerful resource for expert researchers.

Conclusions:

• AQuA Tools provides a much-needed genome arithmetic solution for 3D genomics.
• The tools are expected to lower the barrier for researchers to utilize 3D genomic data.
• AQuA Tools is available at https://github.com/axiotl/aqua-tools for broader adoption and use.