title: BRAT: bisulfite-treated reads analysis tool.
abstract: We present a new, accurate and efficient tool for mapping short reads obtained from the Illumina Genome Analyzer following sodium bisulfite conversion. Our tool, BRAT, supports single and paired-end reads and handles input files containing reads and mates of different lengths. BRAT is faster, maps more unique paired-end reads and has higher accuracy than existing programs. The software package includes tools to end-trim low-quality bases of the reads and to report nucleotide counts for mapped reads on the reference genome.
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: Aleksandr
authors.initials: A
authors.lastname: Levchuk
authors.forename: Karine Le
authors.initials: KL
authors.lastname: Roch
authors.forename: Stefano
authors.initials: S
authors.lastname: Lonardi
mesh_terms: D020869:Gene Expression Profiling / Q000379:methods; D016678:Genome; D023281:Genomics / Q000379:methods*; D012984:Software; D013447:Sulfites / Q000737:chemistry*
chemical_list: D013447:Sulfites; C009279:sodium bisulfite