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

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.

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Genre: Journal Article
Latex : {RRBSMAP}: a Fast, Accurate and User-friendly Alignment Tool for Reduced Representation Bisulfite Sequencing

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 Creators:
Xi, Yuanxin1, Author
Bock, Christoph2, Author           
Müller, Fabian2, Author           
Sun, Deqiang1, Author
Meissner, Alexander1, Author
Li, Wei1, Author
Affiliations:
1External Organizations, ou_persistent22              
2Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society, ou_40046              

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Free keywords: DNA Methylation Embryonic Stem Cells/metabolism Genomics/methods Humans Sequence Alignment/*methods Sequence Analysis, DNA/*methods *Software Sulfites User-Computer Interface
 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.

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Language(s): eng - English
 Dates: 2011-12-062012
 Publication Status: Issued
 Pages: -
 Publishing info: -
 Table of Contents: -
 Rev. Type: -
 Identifiers: PMID: 22155871
PMC: PMC3268241
DOI: 10.1093/bioinformatics/btr668
URI: http://www.ncbi.nlm.nih.gov/pubmed/22155871
BibTex Citekey: Xi2012
Other: Local-ID: 04A4E905EF704B98C1257B160035703B-Xi2012
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Title: Bioinformatics
  Alternative Title : Bioinformatics
Source Genre: Journal
 Creator(s):
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Publ. Info: Oxford, UK : Oxford University Press
Pages: - Volume / Issue: 28 (3) Sequence Number: - Start / End Page: 430 - 432 Identifier: ISSN: 1367-4811
ISSN: 1367-4803