HiC-Pro is an optimized and flexible pipeline designed for processing Hi-C data from raw reads to normalized contact maps. It includes features such as read mapping, detection of valid ligation products, quality controls, and generation of intra- and inter-chromosomal contact maps. The pipeline supports phased genotype data for allele-specific contact map generation and offers a fast implementation of the iterative correction method. HiC-Pro is designed to handle large datasets efficiently, with parallel processing capabilities and memory-efficient data formats. It has been applied to various Hi-C datasets, demonstrating its ability to process large amounts of data in a reasonable time. The source code and documentation are available on GitHub.HiC-Pro is an optimized and flexible pipeline designed for processing Hi-C data from raw reads to normalized contact maps. It includes features such as read mapping, detection of valid ligation products, quality controls, and generation of intra- and inter-chromosomal contact maps. The pipeline supports phased genotype data for allele-specific contact map generation and offers a fast implementation of the iterative correction method. HiC-Pro is designed to handle large datasets efficiently, with parallel processing capabilities and memory-efficient data formats. It has been applied to various Hi-C datasets, demonstrating its ability to process large amounts of data in a reasonable time. The source code and documentation are available on GitHub.