title: BRAT-BW: efficient and accurate mapping of bisulfite-treated reads.
abstract: CONCLUSIONS
  We introduce BRAT-BW, a fast, accurate and memory-efficient tool that maps bisulfite-treated short reads (BS-seq) to a reference genome using the FM-index (Burrows-Wheeler transform). BRAT-BW is significantly more memory efficient and faster on longer reads than current state-of-the-art tools for BS-seq data, without compromising on accuracy. BRAT-BW is a part of a software suite for genome-wide single base-resolution methylation data analysis that supports single and paired-end reads and includes a tool for estimation of methylation level at each cytosine.
  
  
  BACKGROUND
  The software is available in the public domain at http://compbio.cs.ucr.edu/brat/.
authors.affiliation: Department of Computer Science, University of California, Riverside, CA 92521, USA. elenah@cs.ucr.edu
authors.forename: Elena Y
authors.initials: EY
authors.lastname: Harris
authors.forename: Nadia
authors.initials: N
authors.lastname: Ponts
authors.forename: Karine G
authors.initials: KG
authors.lastname: Le Roch
authors.forename: Stefano
authors.initials: S
authors.lastname: Lonardi
mesh_terms: D003596:Cytosine / Q000378:metabolism; D019175:DNA Methylation; D016678:Genome; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites
chemical_list: D013447:Sulfites; D003596:Cytosine; C042345:hydrogen sulfite