title: Probabilistic alignment leads to improved accuracy and read coverage for bisulfite sequencing data.
abstract: BACKGROUND
  DNA methylation has been linked to many important biological phenomena. Researchers have recently begun to sequence bisulfite treated DNA to determine its pattern of methylation. However, sequencing reads from bisulfite-converted DNA can vary significantly from the reference genome because of incomplete bisulfite conversion, genome variation, sequencing errors, and poor quality bases. Therefore, it is often difficult to align reads to the correct locations in the reference genome. Furthermore, bisulfite sequencing experiments have the additional complexity of having to estimate the DNA methylation levels within the sample.
  
  
  RESULTS
  Here, we present a highly accurate probabilistic algorithm, which is an extension of the Genomic Next-generation Universal MAPper to accommodate bisulfite sequencing data (GNUMAP-bs), that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome. GNUMAP-bs integrates uncertainty from read and mapping qualities to help resolve the difference between poor quality bases and the ambiguity inherent in bisulfite conversion. We tested GNUMAP-bs and other commonly-used bisulfite alignment methods using both simulated and real bisulfite reads and found that GNUMAP-bs and other dynamic programming methods were more accurate than the more heuristic methods.
  
  
  CONCLUSIONS
  The GNUMAP-bs aligner is a highly accurate alignment approach for processing the data from bisulfite sequencing experiments. The GNUMAP-bs algorithm is freely available for download at: http://dna.cs.byu.edu/gnumap. The software runs on multiple threads and multiple processors to increase the alignment speed.
authors.affiliation: Division of Computational Biomedicine, Boston University School of Medicine, Boston, MA, USA. wej@bu.edu.
authors.forename: Changjin
authors.initials: C
authors.lastname: Hong
authors.forename: Nathan L
authors.initials: NL
authors.lastname: Clement
authors.forename: Spencer
authors.initials: S
authors.lastname: Clement
authors.forename: Saher Sue
authors.initials: SS
authors.lastname: Hammoud
authors.forename: Douglas T
authors.initials: DT
authors.lastname: Carrell
authors.forename: Bradley R
authors.initials: BR
authors.lastname: Cairns
authors.forename: Quinn
authors.initials: Q
authors.lastname: Snell
authors.forename: Mark J
authors.initials: MJ
authors.lastname: Clement
authors.forename: William Evan
authors.initials: WE
authors.lastname: Johnson
mesh_terms: D000465:Algorithms; D001185:Artificial Intelligence; D001483:Base Sequence; D003198:Computer Simulation; D019175:DNA Methylation; D015894:Genome, Human; D006801:Humans; D011336:Probability; D016415:Sequence Alignment / Q000592:standards*; D017422:Sequence Analysis, DNA; D012984:Software; D013447:Sulfites / Q000737:chemistry* / Q000592:standards
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite