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908686.pdf (7.01 MB)

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2025-10-21

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cc-by (c) Lin, Y.Y. et al., 2025
Si us plau utilitzeu sempre aquest identificador per citar o enllaçar aquest document: https://hdl.handle.net/2445/225034

Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard

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Recurs relacionat

https://doi.org/10.1093/nar/gkaf970

Resum

DNA methylation is a widely studied epigenetic mark and a powerful biomarker of cell type, age, environmental exposures, and disease. Whole-genome sequencing following selective conversion of unmethylated cytosines into thymines via bisulfite treatment or enzymatic methods remains the reference method for DNA methylation profiling genome-wide. While numerous software tools facilitate processing of DNA methylation sequencing reads, a comprehensive benchmarking study has been lacking. In this study, we systematically compared complete computational workflows for processing DNA methylation sequencing data using a dedicated benchmarking dataset generated with five whole-genome profiling protocols. As an evaluation reference, we employed accurate locus-specific measurements from our previous benchmark of targeted DNA methylation assays. Based on this experimental gold-standard assessment and multiple performance metrics, we identified workflows that consistently demonstrated superior performance and revealed major workflow development trends. To ensure the long-term utility of our benchmark, we implemented an interactive workflow execution and data presentation platform, adaptable to user-defined criteria and readily expandable to future software.

Matèries

Biologia computacional, Seqüència de nucleòtids, Epigènesi

Matèries (anglès)

Computational biology, Nucleotide sequence, Epigenesis

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Articles publicats en revistes (Ciències Fisiològiques)

Citació

LIN, Yu-Yu, et al. Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard. Nucleic Acids Research. 2025. Vol. 53, num. 19. ISSN 0305-1048. [consulted: 4 of August of 2026]. Available at: https://hdl.handle.net/2445/225034

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