title: RRBSMAP: a fast, accurate and user-friendly alignment tool for reduced representation bisulfite sequencing.
abstract: CONCLUSIONS
  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.
  
  
  BACKGROUND
  http://rrbsmap.computational-epigenetics.org/ http://code.google.com/p/bsmap/
  
  
  BACKGROUND
  wl1@bcm.tmc.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Division of Biostatistics, Dan L Duncan Cancer Center and Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA.
authors.forename: Yuanxin
authors.initials: Y
authors.lastname: Xi
authors.forename: Christoph
authors.initials: C
authors.lastname: Bock
authors.forename: Fabian
authors.initials: F
authors.lastname: Müller
authors.forename: Deqiang
authors.initials: D
authors.lastname: Sun
authors.forename: Alexander
authors.initials: A
authors.lastname: Meissner
authors.forename: Wei
authors.initials: W
authors.lastname: Li
mesh_terms: D019175:DNA Methylation; D053595:Embryonic Stem Cells / Q000378:metabolism; D023281:Genomics / Q000379:methods; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites; D014584:User-Computer Interface
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite