Details

Autor(en) / Beteiligte

• Abdennur, Nezar
• Fudenberg, Geoffrey
• Flyamer, Ilya M
• Galitsyna, Aleksandra A
• Goloborodko, Anton
• Imakaev, Maxim
• Venev, Sergey V
• Ay, Ferhat

Titel

Pairtools: From sequencing data to chromosome contacts

Ist Teil von

• PLoS computational biology, 2024-05, Vol.20 (5), p.e1012164

Ort / Verlag

United States: Public Library of Science

Erscheinungsjahr

2024

Quelle

EZB-FREE-00999 freely available EZB journals

Beschreibungen/Notizen

• The 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 present pairtools-a flexible suite of tools for contact extraction from sequencing data. Pairtools provides modular command-line interface (CLI) tools that can be flexibly chained into data processing pipelines. The core operations provided by pairtools are parsing of.sam alignments into Hi-C pairs, sorting and removal of PCR duplicates. In addition, pairtools provides auxiliary tools for building feature-rich 3C+ pipelines, including contact pair manipulation, filtration, and quality control. Benchmarking pairtools against popular 3C+ data pipelines shows advantages of pairtools for high-performance and flexible 3C+ analysis. Finally, pairtools provides protocol-specific tools for restriction-based protocols, haplotype-resolved contacts, and single-cell Hi-C. The combination of CLI tools and tight integration with Python data analysis libraries makes pairtools a versatile foundation for a broad range of 3C+ pipelines.