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

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

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.


Benchmarking, Computer Simulation, DNA Methylation, Genome, Human, Humans, Models, Statistical, Sequence Analysis, DNA/methods, Software, Stochastic Processes, Sulfites/chemistry
1367-4803
2371-2373
Rackham, Owen J.L.
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
Dellaportas, Petros
df8947f6-37ea-4e68-8967-eb43f777a5fd
Petretto, Enrico
a8a7d254-ea06-4ab3-ba7e-b653349a29f4
Bottolo, Leonardo
12a7f8db-e00a-42fd-b8f8-01763add4fb9
Rackham, Owen J.L.
8122eb1f-6e9f-4da5-90e1-ce108ccbbcbf
Dellaportas, Petros
df8947f6-37ea-4e68-8967-eb43f777a5fd
Petretto, Enrico
a8a7d254-ea06-4ab3-ba7e-b653349a29f4
Bottolo, Leonardo
12a7f8db-e00a-42fd-b8f8-01763add4fb9

Rackham, Owen J.L., Dellaportas, Petros, Petretto, Enrico and Bottolo, Leonardo (2015) WGBSSuite: simulating whole-genome bisulphite sequencing data and benchmarking differential DNA methylation analysis tools. Bioinformatics, 31 (14), 2371-2373. (doi:10.1093/bioinformatics/btv114).

Record type: 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.


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More information

Accepted/In Press date: 17 February 2015
e-pub ahead of print date: 15 March 2015
Published date: 15 July 2015
Additional Information: © The Author 2015. Published by Oxford University Press.
Keywords: Benchmarking, Computer Simulation, DNA Methylation, Genome, Human, Humans, Models, Statistical, Sequence Analysis, DNA/methods, Software, Stochastic Processes, Sulfites/chemistry

Identifiers

Local EPrints ID: 446734
URI: http://eprints.soton.ac.uk/id/eprint/446734
ISSN: 1367-4803
PURE UUID: 3817b999-6d1b-481b-8d06-943275a8b91e
ORCID for Owen J.L. Rackham: ORCID iD orcid.org/0000-0002-4390-0872

Catalogue record

Date deposited: 19 Feb 2021 17:31
Last modified: 28 Apr 2022 02:30

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Contributors

Author: Petros Dellaportas
Author: Enrico Petretto
Author: Leonardo Bottolo

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