HiC-Pro: an optimized and flexible pipeline for Hi-C data processing.

Area of Science:

• Genomics
• Bioinformatics
• Computational Biology

Background:

• High-throughput chromosome conformation capture (Hi-C) is crucial for understanding 3D genome organization.
• Existing Hi-C data processing pipelines can be computationally intensive and lack flexibility.
• Accurate and efficient processing is essential for reliable downstream analysis of genome architecture.

Purpose of the Study:

• To develop an optimized and flexible pipeline, HiC-Pro, for processing raw Hi-C sequencing reads.
• To generate high-quality, normalized intra- and inter-chromosomal contact maps from Hi-C data.
• To enable the creation of allele-specific contact maps using phased genotype data.

Main Methods:

• HiC-Pro employs a streamlined workflow for mapping reads and identifying valid ligation products.
• It incorporates robust quality control measures throughout the data processing pipeline.
• The pipeline features a fast implementation of the iterative correction method and a memory-efficient data format.

Main Results:

• HiC-Pro successfully processed various Hi-C datasets, demonstrating significant speed and efficiency.
• The pipeline generates normalized contact maps suitable for diverse genomic analyses.
• It provides the capability to construct allele-specific contact maps, enhancing resolution.

Conclusions:

• HiC-Pro offers an efficient, flexible, and user-friendly solution for Hi-C data analysis.
• The pipeline's performance on large datasets makes it suitable for large-scale genomic studies.
• HiC-Pro facilitates deeper insights into 3D genome structure and function.