WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools

Bioinformatics
Owen J L RackhamLeonardo Bottolo

Abstract

As the number of studies looking at differences between DNA methylation increases, there is a growing demand to develop and benchmark statistical methods to analyse these data. To date no objective approach for the comparison of these methods has been developed and as such it remains difficult to assess which analysis tool is most appropriate for a given experiment. As a result, there is an unmet need for a DNA methylation data simulator that can accurately reproduce a wide range of experimental setups, and can be routinely used to compare the performance of different statistical models. We have developed WGBSSuite, a flexible stochastic simulation tool that generates single-base resolution DNA methylation data genome-wide. Several simulator parameters can be derived directly from real datasets provided by the user in order to mimic real case scenarios. Thus, it is possible to choose the most appropriate statistical analysis tool for a given simulated design. To show the usefulness of our simulator, we also report a benchmark of commonly used methods for differential methylation analysis. WGBS code and documentation are available under GNU licence at http://www.wgbssuite.org.uk/ : owen.rackham@imperial.ac.uk or l.bottolo@imperi...Continue Reading

References

Nov 3, 2010·Cell Stem Cell·María J BarreroJuan Carlos Izpisúa Belmonte
May 30, 2012·Nature Reviews. Genetics·Peter A Jones
Oct 5, 2012·Genome Biology·Kasper D HansenRafael A Irizarry
Jun 14, 2013·BMC Bioinformatics·Sheng LiChristopher E Mason
Oct 29, 2013·Statistical Applications in Genetics and Molecular Biology·Michelle R LaceyMelanie Ehrlich

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Citations

Jul 8, 2020·BMC Bioinformatics·Lisardo FernándezJoan Marquez-Molins
Apr 8, 2021·BioMed Research International·Ehsan KhodadadiHossein Samadi Kafil
May 31, 2021·Molecular Ecology Resources·Benjamin MayneSimon Jarman
Jul 29, 2021·Nucleic Acids Research·Timothy J PetersSusan J Clark

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Methods Mentioned

BETA
WGBS
Methylseq

Software Mentioned

BSmooth
WGBSSuite

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