Pairtools is a flexible and efficient suite of tools for extracting chromosome contacts from sequencing data, particularly for Hi-C and other 3C+ protocols. It provides a modular command-line interface (CLI) for processing sequencing data into contact pairs, including parsing .sam/.bam files, sorting, deduplication, and quality control. Pairtools is designed to handle a wide range of 3C+ protocols, including homolog-sensitive, sister chromatid-sensitive, and single-cell Hi-C. It integrates with Python data analysis libraries and is used in high-performance pipelines for 3C+ data processing. Pairtools supports various data formats and provides tools for building feature-rich pipelines, including quality control, filtering, and statistical analysis. It also includes protocol-specific tools for restriction-based protocols, haplotype-resolved contacts, and single-cell Hi-C. Pairtools is available as open-source software and is integrated into the distiller pipeline for high-throughput 3C+ data processing. The software is efficient, scalable, and flexible, making it suitable for a broad range of 3C+ data analysis tasks. Pairtools provides a standardized tabular format for pairs and supports various data processing steps, including sorting, deduplication, and scaling. It also includes tools for quality control, such as scaling analysis and orientation convergence distance calculation. Pairtools is used in multiple pipelines and is available for download and use by researchers in the genomics community.Pairtools is a flexible and efficient suite of tools for extracting chromosome contacts from sequencing data, particularly for Hi-C and other 3C+ protocols. It provides a modular command-line interface (CLI) for processing sequencing data into contact pairs, including parsing .sam/.bam files, sorting, deduplication, and quality control. Pairtools is designed to handle a wide range of 3C+ protocols, including homolog-sensitive, sister chromatid-sensitive, and single-cell Hi-C. It integrates with Python data analysis libraries and is used in high-performance pipelines for 3C+ data processing. Pairtools supports various data formats and provides tools for building feature-rich pipelines, including quality control, filtering, and statistical analysis. It also includes protocol-specific tools for restriction-based protocols, haplotype-resolved contacts, and single-cell Hi-C. Pairtools is available as open-source software and is integrated into the distiller pipeline for high-throughput 3C+ data processing. The software is efficient, scalable, and flexible, making it suitable for a broad range of 3C+ data analysis tasks. Pairtools provides a standardized tabular format for pairs and supports various data processing steps, including sorting, deduplication, and scaling. It also includes tools for quality control, such as scaling analysis and orientation convergence distance calculation. Pairtools is used in multiple pipelines and is available for download and use by researchers in the genomics community.