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RRBSMAP: a Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing

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http://pubman.mpdl.mpg.de/cone/persons/resource/persons44148

Bock,  Christoph
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

http://pubman.mpdl.mpg.de/cone/persons/resource/persons45073

Müller,  Fabian
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

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Citation

Xi, Y., Bock, C., Müller, F., Sun, D., Meissner, A., & Li, W. (2012). RRBSMAP: a Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing. Bioinformatics, 28(3), 430-432. doi:10.1093/bioinformatics/btr668.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0014-C66A-7
Abstract
SUMMARY: Reduced representation bisulfite sequencing (RRBS) is a powerful yet cost-efficient method for studying DNA methylation on a genomic scale. RRBS involves restriction-enzyme digestion, bisulfite conversion and size selection, resulting in DNA sequencing data that require special bioinformatic handling. Here, we describe RRBSMAP, a short-read alignment tool that is designed for handling RRBS data in a user-friendly and scalable way. RRBSMAP uses wildcard alignment, and avoids the need for any preprocessing or post-processing steps. We benchmarked RRBSMAP against a well-validated MAQ-based pipeline for RRBS read alignment and observed similar accuracy but much improved runtime performance, easier handling and better scaling to large sample sets. In summary, RRBSMAP removes bioinformatic hurdles and reduces the computational burden of large-scale epigenome association studies performed with RRBS. AVAILABILITY: http://rrbsmap.computational-epigenetics.org/ http://code.google.com/p/bsmap/ CONTACT: wl1@bcm.tmc.edu SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.