HiC-Pro

HiC-Pro processes high-throughput chromatin conformation capture (Hi-C) sequencing data, converting paired-end Illumina fastq reads into normalized intra- and inter-chromosomal contact maps for chromatin interaction analysis.

Key Features:

• Read mapping and ligation product detection: Maps paired-end sequencing reads and identifies valid ligation products for accurate chromatin interaction assignment.
• Input format support: Processes paired-end Illumina fastq files from raw reads through contact map generation.
• Quality control: Implements quality control measures to assess data reliability.
• Iterative correction method: Incorporates a fast implementation of the iterative correction method for contact map normalization.
• Memory-efficient data format: Uses a memory-efficient format to store Hi-C contact maps for large datasets.
• Allele-specific contact maps: Leverages phased genotype data to construct allele-specific contact maps.

Scientific Applications:

• Chromatin organization and genome architecture: Generates contact maps for analysis of chromatin organization and genome architecture.
• Gene regulation: Facilitates study of chromatin interactions relevant to gene regulation.
• Epigenetic studies: Supports investigations into relationships between chromatin architecture and epigenetic modifications.
• Protocol compatibility: Supports Hi-C data from standard restriction enzyme digestion protocols and enzyme-free methods such as DNase Hi-C.

Methodology:

Performs paired-end Illumina read mapping, valid ligation product identification, quality control, and a fast iterative correction normalization; stores contact maps in a memory-efficient format and can construct allele-specific maps using phased genotype data; can be executed on a single laptop or across a computational cluster using the PBS-Torque scheduler.