title: A new parallel pipeline for DNA methylation analysis of long reads datasets.
abstract: BACKGROUND
  DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete.
  
  
  RESULTS
  In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while yielding a better level of sensitivity, particularly for datasets composed of long reads. This strategy can be exported to other methylation, DNA and RNA analysis tools.
  
  
  CONCLUSIONS
  The developed software tool achieves execution times one order of magnitude shorter than the existing tools, while yielding equal sensitivity for short reads and even better sensitivity for long reads.
authors.affiliation: Departamento de Informática, Universidad de Valencia, Avda. Universidad, s/n, Burjassot Valencia, Spain.
authors.forename: Ricardo
authors.initials: R
authors.lastname: Olanda
authors.affiliation: Departamento de Informática, Universidad de Valencia, Avda. Universidad, s/n, Burjassot Valencia, Spain.
authors.forename: Mariano
authors.initials: M
authors.lastname: Pérez
authors.affiliation: Departamento de Informática, Universidad de Valencia, Avda. Universidad, s/n, Burjassot Valencia, Spain. Juan.Orduna@uv.es.
authors.forename: Juan M
authors.identifier: http://orcid.org/0000-0002-2932-0214
authors.initials: JM
authors.lastname: Orduña
authors.affiliation: Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, s/n, Valencia, Spain.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Tárraga
authors.affiliation: Department of Computational Genomics, Centro de Investigación Príncipe Felipe, Eduardo Primo Yúfera, s/n, Valencia, Spain.
authors.forename: Joaquín
authors.initials: J
authors.lastname: Dopazo
mesh_terms: D019175:DNA Methylation; D030541:Databases, Genetic; D044127:Epigenesis, Genetic; D005786:Gene Expression Regulation; D015894:Genome, Human; D006801:Humans; D009154:Mutation; D012680:Sensitivity and Specificity; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
keywords: DNA methylation; High performance computing; Parallel pipeline