WGBS Suite: Simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools

5Citations
Citations of this article
59Readers
Mendeley users who have this article in their library.

Abstract

Motivation: 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.<br />Results: 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.<br />Availability and implementation: WGBS code and documentation are available under GNU licence at http://www.wgbssuite.org.uk/<br />Contact: owen.rackham@imperial.ac.uk or l.bottolo@imperial.ac.uk<br />Supplementary information: Supplementary data are available at Bioinformatics online.

Cite

CITATION STYLE

APA

Rackham, O. J. L., Dellaportas, P., Petretto, E., & Bottolo, L. (2015). WGBS Suite: Simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools. Bioinformatics, 31(14), 2371–2373. https://doi.org/10.1093/bioinformatics/btv114

Register to see more suggestions

Mendeley helps you to discover research relevant for your work.

Already have an account?

Save time finding and organizing research with Mendeley

Sign up for free