title: BatMeth: improved mapper for bisulfite sequencing reads on DNA methylation.
abstract: DNA methylation plays a crucial role in higher organisms. Coupling bisulfite treatment with next generation sequencing enables the interrogation of 5-methylcytosine sites in the genome. However, bisulfite conversion introduces mismatches between the reads and the reference genome, which makes mapping of Illumina and SOLiD reads slow and inaccurate. BatMeth is an algorithm that integrates novel Mismatch Counting, List Filtering, Mismatch Stage Filtering and Fast Mapping onto Two Indexes components to improve unique mapping rate, speed and precision. Experimental results show that BatMeth is faster and more accurate than existing tools. BatMeth is freely available at http://code.google.com/p/batmeth/.
authors.forename: Jing-Quan
authors.initials: JQ
authors.lastname: Lim
authors.forename: Chandana
authors.initials: C
authors.lastname: Tennakoon
authors.forename: Guoliang
authors.initials: G
authors.lastname: Li
authors.forename: Eleanor
authors.initials: E
authors.lastname: Wong
authors.forename: Yijun
authors.initials: Y
authors.lastname: Ruan
authors.forename: Chia-Lin
authors.initials: CL
authors.lastname: Wei
authors.forename: Wing-Kin
authors.initials: WK
authors.lastname: Sung
mesh_terms: D044503:5-Methylcytosine / Q000378:metabolism*; D000465:Algorithms; D018899:CpG Islands; D019175:DNA Methylation; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D017422:Sequence Analysis, DNA / Q000379:methods*; D013447:Sulfites
chemical_list: D013447:Sulfites; D044503:5-Methylcytosine; C042345:hydrogen sulfite