WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools
Author(s)
Rackham, Owen JL
Dellaportas, Petros
Petretto, Enrico
Bottolo, Leonardo
Type
Journal Article
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.
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.
Availability and implementation: WGBS code and documentation are available under GNU licence at http://www.wgbssuite.org.uk/
Contact: owen.rackham@imperial.ac.uk or l.bottolo@imperial.ac.uk
Supplementary information:Supplementary data are available at Bioinformatics online.
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.
Availability and implementation: WGBS code and documentation are available under GNU licence at http://www.wgbssuite.org.uk/
Contact: owen.rackham@imperial.ac.uk or l.bottolo@imperial.ac.uk
Supplementary information:Supplementary data are available at Bioinformatics online.
Date Issued
2015-07-15
Date Acceptance
2015-02-17
Citation
Bioinformatics, 2015, 31 (14), pp.2371-2373
ISSN
1367-4803
Publisher
Oxford University Press (OUP)
Start Page
2371
End Page
2373
Journal / Book Title
Bioinformatics
Volume
31
Issue
14
Copyright Statement
© The Author 2015. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
Identifier
http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcApp=PARTNER_APP&SrcAuth=LinksAMR&KeyUT=WOS:000358173500018&DestLinkType=FullRecord&DestApp=ALL_WOS&UsrCustomerID=1ba7043ffcc86c417c072aa74d649202
Subjects
Science & Technology
Life Sciences & Biomedicine
Technology
Physical Sciences
Biochemical Research Methods
Biotechnology & Applied Microbiology
Computer Science, Interdisciplinary Applications
Mathematical & Computational Biology
Statistics & Probability
Biochemistry & Molecular Biology
Computer Science
Mathematics
PROFILES
Publication Status
Published
Date Publish Online
2015-03-15