Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2012 Feb 1;28(3):430-2.
doi: 10.1093/bioinformatics/btr668. Epub 2011 Dec 6.

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing

Yuanxin Xi  1 , Christoph Bock, Fabian Müller, Deqiang Sun, Alexander Meissner, Wei Li
Affiliations

RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing

Yuanxin Xi et al. Bioinformatics. .

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.

PubMed Disclaimer

Similar articles

See all similar articles

Cited by

See all "Cited by" articles

References

    1. Baranzini S.E., et al. Genome, epigenome and RNA sequences of monozygotic twins discordant for multiple sclerosis. Nature. 2010;464:1351–1356. - PMC - PubMed
    1. Bock C., et al. BiQ Analyzer: visualization and quality control for DNA methylation data from bisulfite sequencing. Bioinformatics. 2005;21:4067–4068. - PubMed
    1. Bock C., et al. Quantitative comparison of genome-wide DNA methylation mapping technologies. Nat. Biotechnol. 2010;28:1106–1114. - PMC - PubMed
    1. Bock C., et al. Reference maps of human ES and iPS cell variation enable high-throughput characterization of pluripotent cell lines. Cell. 2011;144:439–452. - PMC - PubMed
    1. Carone B.R., et al. Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals. Cell. 2010;143:1084–1096. - PMC - PubMed

Publication types