2026-04-14T04:23:15Zhttps://recercat.cat/oai/requestoai:recercat.cat:2445/2250342026-04-10T21:57:58Zcom_2072_1057col_2072_478799col_2072_478917
Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
Lin, Yu-Yu
Breuer, Kersten
Weichenhan, Dieter
Lafrenz, Pascal
Sarnataro, Antonella
Wilk, Agata
Chepeleva, Maryna
Mücke, Oliver
Schönung, Maximilian
Petermann, Franziska
Kensche, Philip Reiner
Weiser, Lena
Thommen, Frank
Giacomelli, Gideon
Nordstroem, Karl
Gonzalez-Avalos, Edahi
Merkel, Angelika
Kretzmer, Helene
Fischer, Jonas
Krämer, Stephen
Iskar, Murat
Wolf, Stephan
Buchhalter, Ivo
Esteller, Manel, 1968-
Lawerenz, Christian
Twardziok, Sven
Zapatka, Marc
Hovestadt, Volker
Schlesner, Matthias
Schulz, Marcel H.
Hoffmann, Steve
Gerhauser, Clarissa
Walter, Jörn
Hartmann, Mark
Lipka, Daniel B.
Assenov, Yassen
Bock, Christoph
Plass, Christoph
Toth, Reka
Lutsik, Pavlo
Biologia computacional
Seqüència de nucleòtids
Epigènesi
Computational biology
Nucleotide sequence
Epigenesis
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.
2025-12-17T16:26:58Z
2025-12-17T16:26:58Z
2025-10-21
2025-12-17T16:26:58Z
info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
Reproducció del document publicat a: https://doi.org/10.1093/nar/gkaf970
Nucleic Acids Research, 2025, vol. 53, num.19
https://doi.org/10.1093/nar/gkaf970
cc-by (c) Lin, Y.Y. et al., 2025
https://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
Oxford University Press
Articles publicats en revistes (Ciències Fisiològiques)