HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. It maps reads, detects valid ligation products, performs quality controls, and generates intra- and inter-chromosomal contact maps. HiC-Pro includes a fast implementation of the iterative correction method and uses a memory-efficient data format for Hi-C contact maps. It can also use phased genotype data to build allele-specific contact maps. HiC-Pro was tested on various Hi-C datasets, demonstrating its ability to process large data efficiently. The software is available at https://github.com/nservant/HiC-Pro. Hi-C is a high-throughput method for mapping chromatin interactions. It involves sequencing pairs of interacting DNA fragments. Hi-C data typically requires millions to billions of paired-end reads. HiC-Pro is designed to handle large datasets efficiently, with parallel processing capabilities. It is optimized for high-resolution data and includes a fast implementation of the iterative correction method. HiC-Pro processes Hi-C data through four main steps: read alignment, detection and filtering of valid interaction products, binning, and contact map normalization. It uses a two-step mapping strategy to rescue and align reads. HiC-Pro can generate allele-specific contact maps using phased genotype data. It is also capable of generating high-resolution contact maps and normalizing them efficiently. HiC-Pro is compared with other Hi-C processing tools such as HOMER, HICUP, HiC-inspector, HiCdat, and HiC-box. HiC-Pro is more efficient than these tools in terms of processing time and memory usage. It is also able to generate allele-specific contact maps, which other tools cannot do. HiC-Pro is optimized for high-resolution data and provides a memory-efficient format for contact maps. HiC-Pro is implemented in Python and C++ and uses efficient data structures such as compressed sparse row matrices for contact count data. It is designed to be user-friendly and can be run on a single command line. It is also modular and allows users to focus on specific parts of the processing workflow. HiC-Pro is freely available under the BSD license and is suitable for both research and clinical applications. It is a flexible and efficient tool for processing Hi-C data and is recommended for use in large-scale studies.HiC-Pro is an optimized and flexible pipeline for processing Hi-C data from raw reads to normalized contact maps. It maps reads, detects valid ligation products, performs quality controls, and generates intra- and inter-chromosomal contact maps. HiC-Pro includes a fast implementation of the iterative correction method and uses a memory-efficient data format for Hi-C contact maps. It can also use phased genotype data to build allele-specific contact maps. HiC-Pro was tested on various Hi-C datasets, demonstrating its ability to process large data efficiently. The software is available at https://github.com/nservant/HiC-Pro. Hi-C is a high-throughput method for mapping chromatin interactions. It involves sequencing pairs of interacting DNA fragments. Hi-C data typically requires millions to billions of paired-end reads. HiC-Pro is designed to handle large datasets efficiently, with parallel processing capabilities. It is optimized for high-resolution data and includes a fast implementation of the iterative correction method. HiC-Pro processes Hi-C data through four main steps: read alignment, detection and filtering of valid interaction products, binning, and contact map normalization. It uses a two-step mapping strategy to rescue and align reads. HiC-Pro can generate allele-specific contact maps using phased genotype data. It is also capable of generating high-resolution contact maps and normalizing them efficiently. HiC-Pro is compared with other Hi-C processing tools such as HOMER, HICUP, HiC-inspector, HiCdat, and HiC-box. HiC-Pro is more efficient than these tools in terms of processing time and memory usage. It is also able to generate allele-specific contact maps, which other tools cannot do. HiC-Pro is optimized for high-resolution data and provides a memory-efficient format for contact maps. HiC-Pro is implemented in Python and C++ and uses efficient data structures such as compressed sparse row matrices for contact count data. It is designed to be user-friendly and can be run on a single command line. It is also modular and allows users to focus on specific parts of the processing workflow. HiC-Pro is freely available under the BSD license and is suitable for both research and clinical applications. It is a flexible and efficient tool for processing Hi-C data and is recommended for use in large-scale studies.