Pairtools: from sequencing data to chromosome contacts

Abstract

AbstractThe field of 3D genome organization produces large amounts of sequencing data from Hi-C and a rapidly-expanding set of other chromosome conformation protocols (3C+). Massive and heterogeneous 3C+ data require high-performance and flexible processing of sequenced reads into contact pairs. To meet these challenges, we presentpairtools– a flexible suite of tools for contact extraction from sequencing data.Pairtoolsprovides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines.Pairtoolsprovides both crucial core tools as well as auxiliary tools for building feature-rich 3C+ pipelines, including contact pair manipulation, filtration, and quality control. Benchmarkingpairtoolsagainst popular 3C+ data pipelines shows advantages ofpairtoolsfor high-performance and flexible 3C+ analysis. Finally,pairtoolsprovides protocol-specific tools for multi-way contacts, haplotype-resolved contacts, and single-cell Hi-C. The combination of CLI tools and tight integration with Python data analysis libraries makespairtoolsa versatile foundation for a broad range of 3C+ pipelines.