title: BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
abstract: BACKGROUND
  DNA methylation is an important epigenetic modification involved in many biological processes. Bisulfite treatment coupled with high-throughput sequencing provides an effective approach for studying genome-wide DNA methylation at base resolution. Libraries such as whole genome bisulfite sequencing (WGBS) and reduced represented bisulfite sequencing (RRBS) are widely used for generating DNA methylomes, demanding efficient and versatile tools for aligning bisulfite sequencing data.
  
  
  RESULTS
  We have developed BS-Seeker2, an updated version of BS Seeker, as a full pipeline for mapping bisulfite sequencing data and generating DNA methylomes. BS-Seeker2 improves mappability over existing aligners by using local alignment. It can also map reads from RRBS library by building special indexes with improved efficiency and accuracy. Moreover, BS-Seeker2 provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing the overestimation of DNA methylation levels. We also defined CGmap and ATCGmap file formats for full representations of DNA methylomes, as part of the outputs of BS-Seeker2 pipeline together with BAM and WIG files.
  
  
  CONCLUSIONS
  Our evaluations on the performance show that BS-Seeker2 works efficiently and accurately for both WGBS data and RRBS data. BS-Seeker2 is freely available at http://pellegrini.mcdb.ucla.edu/BS_Seeker2/ and the Galaxy server.
authors.forename: Weilong
authors.initials: W
authors.lastname: Guo
authors.forename: Petko
authors.initials: P
authors.lastname: Fiziev
authors.forename: Weihong
authors.initials: W
authors.lastname: Yan
authors.forename: Shawn
authors.initials: S
authors.lastname: Cokus
authors.forename: Xueguang
authors.initials: X
authors.lastname: Sun
authors.forename: Michael Q
authors.initials: MQ
authors.lastname: Zhang
authors.affiliation: Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA. paoyang@gate.sinica.edu.tw.
authors.forename: Pao-Yang
authors.initials: PY
authors.lastname: Chen
authors.forename: Matteo
authors.initials: M
authors.lastname: Pellegrini
mesh_terms: D018899:CpG Islands / Q000235:genetics; D019175:DNA Methylation / Q000235:genetics*; D015894:Genome, Human; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013447:Sulfites / Q000737:chemistry
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite