{"doi":"10.1371/journal.pcbi.1012164","title":"Pairtools: From sequencing data to chromosome contacts","abstract":"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.","journal":"PLoS Computational Biology","year":2024,"id":416203,"datarank":0.8150583005331361,"base_score":5.43372200355424,"endowment":5.43372200355424,"self_citation_contribution":0.8150583005331361,"citation_network_contribution":0.0,"self_endowment_contribution":0.8150583005331361,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":228,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.956,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2024-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":109516,"name":"Nezar Abdennur","orcid":"0000-0001-5814-0864","position":1,"is_corresponding":false},{"id":87758,"name":"Geoffrey Fudenberg","orcid":"0000-0001-5905-6517","position":2,"is_corresponding":false},{"id":553444,"name":"Ilya M. Flyamer","orcid":"0000-0002-4892-4208","position":3,"is_corresponding":false},{"id":873582,"name":"Aleksandra A. Galitsyna","orcid":"0000-0001-8969-5694","position":4,"is_corresponding":false},{"id":983035,"name":"Anton Goloborodko","orcid":"0000-0002-2210-8616","position":5,"is_corresponding":false},{"id":355547,"name":"Maxim Imakaev","orcid":"0000-0002-5320-2728","position":6,"is_corresponding":false},{"id":109515,"name":"Sergey V. Venev","orcid":"0000-0002-1507-7460","position":7,"is_corresponding":false},{"id":983720,"name":"Open2C","orcid":null,"position":0,"is_corresponding":true}],"reference_count":68,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:56:20.964471Z","pmid":"38809952","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}