The DOI matches its Crossref record; 75 of the 75 references it cites were found in a registry or an index.
Pairtools: From sequencing data to chromosome contacts
Open accessAbstract
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.
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The Sequence Alignment/Map format and SAMtools
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SciPy 1.0: fundamental algorithms for scientific computing in Python
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Twelve years of SAMtools and BCFtools
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SciPy 1.0: fundamental algorithms for scientific computing in Python
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Self-citation
Metadata
- Authors
- Open2C, Abdennur, N., Fudenberg, G., Flyamer, I. M., Galitsyna, A. A., Goloborodko, A., Imakaev, M., & Venev, S. V.
- Venue
- PLOS Computational Biology
- Publisher
- Public Library of Science (PLoS)
- Published
- 2024-05-29
- Volume
- 20
- Issue
- 5
- Pages
- e1012164
- ISSN
- 1553-734X (ISSN-L)
- 1553-7358
- OpenAlex
- W4399118709
- Cited by
- 279
- References
- 75
- FWCI
- 30.21
- Type
- journal article
- Language
- en
- Open access
- gold
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