ArticleBriefings in bioinformatics2025
Pore-C Pipeline-Toolbox: a comprehensive pipeline for Pore-C data analysis.
Article in Briefings in bioinformatics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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6 authors.
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Abstract
Three-dimensional (3D) genomic architecture is crucial for the regulation of different biological processes, and the study of multi-way chromatin structures represents a cutting-edge area in this field. Pore-C is an advanced experimental technique integrating chromosome conformation capture (3C) with Nanopore long-read sequencing, which can effectively capture complex multi-way chromatin contacts across the genome. Due to the absence of comprehensive and dedicated tools, the analysis of Pore-C data remains challenging, restricting its broader application. To address this limitation, we developed Pore-C Pipeline Toolbox (PPL-Toolbox), a specialized software for a comprehensive analysis of multi-way chromatin interactions from Pore-C data. PPL-Toolbox incorporates a suite of optimized modules, including quality control, multi-way interaction extraction, noise reduction for multi-way contacts, advanced visualization tools for multi-way contacts, and haplotype map generation. Evaluation on both simulated and real datasets demonstrates that the PPL-Toolbox outperforms existing methods by providing a more comprehensive set of results. PPL-Toolbox is expected to become a powerful and versatile tool, driving advance in multi-way 3D genomics research, and enabling new discoveries in the field. PPL-Toolbox is publicly available on GitHub (https://github.com/versarchey/PPL-Toolbox).
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