title: BRAT-nova: fast and accurate mapping of bisulfite-treated reads.
abstract: In response to increasing amounts of sequencing data, faster and faster aligners need to become available. Here, we introduce BRAT-nova, a completely rewritten and improved implementation of the mapping tool BRAT-BW for bisulfite-treated reads (BS-Seq). BRAT-nova is very fast and accurate. On the human genome, BRAT-nova is 2-7 times faster than state-of-the-art aligners, while maintaining the same percentage of uniquely mapped reads and space usage. On synthetic reads, BRAT-nova is 2-8 times faster than state-of-the-art aligners while maintaining similar mapping accuracy, methylation call accuracy, methylation level accuracy and space efficiency.
  
  
  
  The software is available in the public domain at http://compbio.cs.ucr.edu/brat/
  
  
  
  elenah@cs.ucr.edu
  
  
  
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Computer Science, California State University, Chico, CA 95929, USA.
authors.forename: Elena Y
authors.initials: EY
authors.lastname: Harris
authors.affiliation: Department of Computer Science and Eng, University of California, Riverside, CA 92521, USA.
authors.forename: Rachid
authors.initials: R
authors.lastname: Ounit
authors.affiliation: Department of Computer Science and Eng, University of California, Riverside, CA 92521, USA.
authors.forename: Stefano
authors.initials: S
authors.lastname: Lonardi
mesh_terms: D002874:Chromosome Mapping; D019175:DNA Methylation; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software