Pipeline Olympics: continuable benchmarking of computational workflows for DNA methylation sequencing data against an experimental gold standard
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.
Authors
- Pavlo Lutsik (ORCID: https://orcid.org/0000-0001-9383-8555)
- Clarissa Gerhäuser (ORCID: https://orcid.org/0000-0002-5792-3901)
- Manel Esteller (ORCID: https://orcid.org/0000-0003-4490-6093)
- Antonella Sarnataro (ORCID: https://orcid.org/0009-0002-5195-697X)
- Mark Hartmann (ORCID: https://orcid.org/0000-0002-4072-4658)
- Daniel B. Lipka (ORCID: https://orcid.org/0000-0001-5081-7869)
- Christoph Plass (ORCID: https://orcid.org/0000-0003-2554-3952)
- Lena Weiser
- Angelika Merkel (ORCID: https://orcid.org/0000-0001-5164-6803)
- Maximilian Schönung (ORCID: https://orcid.org/0000-0002-9778-9698)
- Edahí González‐Avalos (ORCID: https://orcid.org/0000-0002-6817-4854)
- Stephan Wolf
- Sven Twardziok (ORCID: https://orcid.org/0000-0002-0326-5704)
- Oliver Mücke
- Gideon Giacomelli
- Kersten Breuer (ORCID: https://orcid.org/0000-0003-3716-7739)
- Dieter Weichenhan (ORCID: https://orcid.org/0000-0002-7915-412X)
- Stephen Krämer (ORCID: https://orcid.org/0000-0002-9585-9330)
- Christian Lawerenz
- Jörn Walter (ORCID: https://orcid.org/0000-0003-0563-7417)
- Marc Zapatka (ORCID: https://orcid.org/0000-0001-8287-5967)
- Christoph Bock (ORCID: https://orcid.org/0000-0001-6091-3088)
- Maryna Chepeleva (ORCID: https://orcid.org/0000-0003-3036-4916)
- Réka Tóth (ORCID: https://orcid.org/0000-0003-4099-5359)
- Karl Nordstroem
- Ivo Buchhalter (ORCID: https://orcid.org/0000-0003-0764-5832)
- Steve Hoffmann (ORCID: https://orcid.org/0000-0002-5239-7201)
- Pascal Lafrenz (ORCID: https://orcid.org/0000-0002-3791-3474)
- Matthias Schlesner (ORCID: https://orcid.org/0000-0002-5896-4086)
- Yassen Assenov (ORCID: https://orcid.org/0000-0002-6992-2092)
- Volker Hovestadt (ORCID: https://orcid.org/0000-0002-3480-6649)
- Franziska Petermann (ORCID: https://orcid.org/0000-0002-3145-2304)
- Marcel H. Schulz (ORCID: https://orcid.org/0000-0002-1252-3656)
- Murat Iskar (ORCID: https://orcid.org/0000-0001-8603-4313)
- Helene Kretzmer (ORCID: https://orcid.org/0000-0002-0723-4980)
- Jonas Fischer (ORCID: https://orcid.org/0000-0003-4225-9734)
- Yu‐Yu Lin (ORCID: https://orcid.org/0000-0001-9833-580X)
- Frank Thommen
- Philip Kensche
- Agata Wilk
Institutions
- Broad Institute (US)
- Goethe University Frankfurt (DE)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- Boston Children's Hospital (US)
- La Jolla Institute for Immunology (US)
- Leipzig University of Applied Sciences (DE)
- Austrian Research Institute for Artificial Intelligence (AT)
- Koblenz University of Applied Sciences (DE)
- University of Augsburg (DE)
- German Cancer Research Center (DE)
- Heidelberg University (DE)
- University Hospital Heidelberg (DE)
- Josep Carreras Leukaemia Research Institute (ES)
- Luxembourg Institute of Health (LU)
- Max Planck Institute for Informatics (DE)
- National Center for Tumor Diseases (DE)
- Department of Physiological Sciences (RU)
- Dana-Farber Cancer Institute (US)
- CeMM Research Center for Molecular Medicine (AT)
- Leibniz Institute on Aging - Fritz Lipmann Institute (FLI) (DE)
- DIPF | Leibniz Institute for Research and Information in Education (DE)
- Berlin Institute of Health at Charité - Universitätsmedizin Berlin (DE)
- Centro Nacional de Análisis Genómico (ES)
- Max Planck Institute for Molecular Genetics (DE)
- Boston Children's Museum (US)
- Centro de Investigación Biomédica en Red de Cáncer (ES)
- Life University (US)
- Heidelberg University (US)
- Epigenomics (Germany) (DE)
- Saarland University (DE)
- Leipzig University (DE)
- Otto-von-Guericke-Universität Magdeburg (DE)
- KU Leuven (BE)
Publication Details
- Journal
- Nucleic Acids Research
- Published
- 2025-09-12
- DOI
- https://doi.org/10.1093/nar/gkaf970
- Primary Topic
- Epigenetics and DNA Methylation
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- Bundesministerium für Bildung und Forschung