Galaxy HiCExplorer: a web server for reproducible Hi-C data analysis, quality control and visualization

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• Understanding the three-dimensional (3D) organization of chromatin is crucial for gene regulation.
• Hi-C technology provides genome-wide insights into chromatin interactions.
• Analyzing Hi-C data requires specialized bioinformatics expertise and computational resources.

Purpose of the Study:

• To develop an accessible web server for comprehensive Hi-C data analysis and visualization.
• To enable researchers with limited bioinformatics experience to perform complex chromatin conformation studies.
• To integrate various analysis steps, from raw data processing to the identification of structural elements.

Main Methods:

• Galaxy HiCExplorer web server implementation.
• Integration of deeptools functionalities for Hi-C data processing.
• Workflow automation for mapping, contact matrix generation, quality assessment, and data correction.
• Algorithms for the identification of topological associated domains (TADs) and A/B compartments.

Main Results:

• A user-friendly, integrated platform for the complete analysis of Hi-C data.
• Generation of publication-quality visualizations of chromatin contact matrices, TADs, and A/B compartments.
• Successful identification of genomic structural features from Hi-C data.

Conclusions:

• Galaxy HiCExplorer democratizes Hi-C data analysis, making 3D genome studies accessible to a broader scientific audience.
• The platform streamlines complex bioinformatics workflows, accelerating discoveries in chromatin organization and function.
• Provides a robust and freely available resource for advancing research in genome architecture.