Lin, Yu-YuBreuer, KerstenWeichenhan, DieterLafrenz, PascalSarnataro, AntonellaWilk, AgataChepeleva, MarynaMücke, OliverSchönung, MaximilianPetermann, FranziskaKensche, Philip ReinerWeiser, LenaThommen, FrankGiacomelli, GideonNordstroem, KarlGonzalez-Avalos, EdahiMerkel, AngelikaKretzmer, HeleneFischer, JonasKrämer, StephenIskar, MuratWolf, StephanBuchhalter, IvoEsteller, Manel, 1968-Lawerenz, ChristianTwardziok, SvenZapatka, MarcHovestadt, VolkerSchlesner, MatthiasSchulz, Marcel H.Hoffmann, SteveGerhauser, ClarissaWalter, JörnHartmann, MarkLipka, Daniel B.Assenov, YassenBock, ChristophPlass, ChristophToth, RekaLutsik, Pavlo2025-12-172025-12-172025-10-210305-1048https://hdl.handle.net/2445/225034DNA 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.19 p.application/pdfengcc-by (c) Lin, Y.Y. et al., 2025https://creativecommons.org/licenses/by/4.0/Biologia computacionalSeqüència de nucleòtidsEpigènesiComputational biologyNucleotide sequenceEpigenesisinfo:eu-repo/semantics/article7629552025-12-17info:eu-repo/semantics/openAccess41118575