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dc.contributor.authorAbdennur, Nezar
dc.contributor.authorFudenberg, Geoffrey
dc.contributor.authorFlyamer, Ilya M
dc.contributor.authorGalitsyna, Aleksandra A
dc.contributor.authorGoloborodko, Anton
dc.contributor.authorImakaev, Maxim
dc.contributor.authorVenev, Sergey V
dc.date.accessioned2024-07-02T15:39:13Z
dc.date.available2024-07-02T15:39:13Z
dc.date.issued2024-05-29
dc.identifier.citationOpen2C; Abdennur N, Fudenberg G, Flyamer IM, Galitsyna AA, Goloborodko A, Imakaev M, Venev SV. Pairtools: From sequencing data to chromosome contacts. PLoS Comput Biol. 2024 May 29;20(5):e1012164. doi: 10.1371/journal.pcbi.1012164. PMID: 38809952; PMCID: PMC11164360.en_US
dc.identifier.eissn1553-7358
dc.identifier.doi10.1371/journal.pcbi.1012164en_US
dc.identifier.pmid38809952
dc.identifier.urihttp://hdl.handle.net/20.500.14038/53544
dc.description.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 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.en_US
dc.language.isoen
dc.relationThis article is based on a previously available preprint in bioRxiv, https://doi.org/10.1101/2023.02.13.528389.en_US
dc.relation.ispartofPLoS Computational Biologyen_US
dc.relation.urlhttps://doi.org/10.1371/journal.pcbi.1012164en_US
dc.rightsCopyright: © 2024 Open2C et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.; Attribution 4.0 Internationalen_US
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/*
dc.subjectGenomicsen_US
dc.subjectSequence alignmenten_US
dc.subjectData processingen_US
dc.subjectDNA librariesen_US
dc.subjectDNA fragment ligationen_US
dc.subjectQuality controlen_US
dc.subjectChromosome pairsen_US
dc.subjectComputer softwareen_US
dc.titlePairtools: From sequencing data to chromosome contactsen_US
dc.typeJournal Articleen_US
dc.source.journaltitlePLoS computational biology
dc.source.volume20
dc.source.issue5
dc.source.beginpagee1012164
dc.source.endpage
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryUnited States
dc.source.countryUnited States
dc.identifier.journalPLoS computational biology
refterms.dateFOA2024-07-02T15:39:15Z
dc.contributor.departmentGenomics and Computational Biologyen_US
dc.contributor.departmentProgram in Bioinformatics and Integrative Biologyen_US
dc.contributor.departmentSystems Biologyen_US


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Copyright: © 2024 Open2C et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.; Attribution 4.0 International
Except where otherwise noted, this item's license is described as Copyright: © 2024 Open2C et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.; Attribution 4.0 International