title: A parallel and sensitive software tool for methylation analysis on multicore platforms.
abstract: BACKGROUND
  DNA methylation analysis suffers from very long processing time, as the advent of Next-Generation Sequencers has shifted the bottleneck of genomic studies from the sequencers that obtain the DNA samples to the software that performs the analysis of these samples. The existing software for methylation analysis does not seem to scale efficiently neither with the size of the dataset nor with the length of the reads to be analyzed. As it is expected that the sequencers will provide longer and longer reads in the near future, efficient and scalable methylation software should be developed.
  
  
  RESULTS
  We present a new software tool, called HPG-Methyl, which efficiently maps bisulphite sequencing reads on DNA, analyzing DNA methylation. The strategy used by this software consists of leveraging the speed of the Burrows-Wheeler Transform to map a large number of DNA fragments (reads) rapidly, as well as the accuracy of the Smith-Waterman algorithm, which is exclusively employed to deal with the most ambiguous and shortest reads. Experimental results on platforms with Intel multicore processors show that HPG-Methyl significantly outperforms in both execution time and sensitivity state-of-the-art software such as Bismark, BS-Seeker or BSMAP, particularly for long bisulphite reads.
  
  
  METHODS
  Software in the form of C libraries and functions, together with instructions to compile and execute this software. Available by sftp to anonymous@clariano.uv.es (password 'anonymous').
  
  
  BACKGROUND
  juan.orduna@uv.es or jdopazo@cipf.es.
authors.affiliation: Department of Computational Genomics, Centro de Investigación Príncipe Felipe.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Tárraga
authors.affiliation: Departamento de Informática, Universidad de Valencia and.
authors.forename: Mariano
authors.initials: M
authors.lastname: Pérez
authors.affiliation: Departamento de Informática, Universidad de Valencia and.
authors.forename: Juan M
authors.initials: JM
authors.lastname: Orduña
authors.affiliation: DISCA, Universidad Politécnica de Valencia, Valencia, Spain.
authors.forename: José
authors.initials: J
authors.lastname: Duato
authors.affiliation: Department of Computational Genomics, Centro de Investigación Príncipe Felipe.
authors.forename: Ignacio
authors.initials: I
authors.lastname: Medina
authors.affiliation: Department of Computational Genomics, Centro de Investigación Príncipe Felipe.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D019175:DNA Methylation / Q000235:genetics*; D030541:Databases, Genetic; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D008969:Molecular Sequence Data; D009154:Mutation / Q000235:genetics; D059645:Mutation Rate; D012984:Software; D013447:Sulfites; D013997:Time Factors
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite