ArticlePLoS computational biology2024
Pairtools: From sequencing data to chromosome contacts.
Article in PLoS computational biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 215 papers.
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Who cites it
215 citing papers in PubMed.
- First chromosome-scale genome of Cornus kousa K2‡.G3 (Bethesda, Md.) · 2026Article
- A Mid-Atlantic Brook Trout (Salvelinus fontinalis) genome to advance conservation and comparative genomics.G3 (Bethesda, Md.) · 2026Article
- Cell-cycle-resolved Hi-C reveals unexpected plasticity of A/B compartments across interphase.eLife · 2026Article
- Nested TAD hierarchy defines cohesion zones on replicated chromosomes.The EMBO journal · 2026Article
- Cohesin promotes genomic stability by suppressing unequal sister chromatid exchange.bioRxiv : the preprint server for biology · 2026Article
- De novo structural variants in autism spectrum disorder disrupt distal regulatory interactions of neuronal genes.Genome research · 2026Article
- dcHiChIP: a comprehensive Nextflow-based pipeline for multiscale analysis of chromatin architecture from HiChIP data.Bioinformatics (Oxford, England) · 2026Article
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- Bridging-driven condensation by eukaryotic SMC complexes is a conserved feature of genome organization.Nucleic acids research · 2026Article
- Finishing a complete giraffe genome from telomere to telomere with Verkko-Fillet.Cell genomics · 2026Article
- Chromosome-scale genome assembly and annotation of the white star apple (Gambeya albida).Scientific data · 2026Article
- map3C: a computational tool for processing multiomic single-cell Hi-C data.Bioinformatics (Oxford, England) · 2026Article
- Developmental expression of the skeletal muscle determination gene,bioRxiv : the preprint server for biology · 2026Article
- Evolution of compound eye cell types shapes visual behaviors acrossbioRxiv : the preprint server for biology · 2026Article
- Decoding 3D chromatin architecture reveals distinct enhancer classes underlying hierarchical gene regulation in prostate cancer.Genome biology · 2026Article
- A 3D genome atlas of human tonsil and the role of loop extrusion in B cell somatic hypermutation.Science (New York, N.Y.) · 2026Article
- Human Alu loci gain enhancer-type epigenetic modifications in monocytes during response to bacterial LPS.Epigenetics & chromatin · 2026Article
- CAD-C: An engineered nuclease enables repair-freebioRxiv : the preprint server for biology · 2026Article
- A de novo genome assembly of an Angelman syndrome pig (Sus scrofa domesticus) model to resolve SNHG14.The Journal of heredity · 2026Article
- Chromosome-level reference genome of a foundational California native legume, Acmispon strigosus.The Journal of heredity · 2026Article
155 more citing papers are in PubMed but not listed here.
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8 authors.
Funding
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.