title: Pash 3.0: A versatile software package for read mapping and integrative analysis of genomic and epigenomic variation using massively parallel DNA sequencing.
abstract: BACKGROUND
  Massively parallel sequencing readouts of epigenomic assays are enabling integrative genome-wide analyses of genomic and epigenomic variation. Pash 3.0 performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing.
  
  
  RESULTS
  Pash 3.0 generally matches the accuracy and speed of niche programs for fast mapping of short reads, and exceeds their performance on longer reads generated by a new generation of massively parallel sequencing technologies. By exploiting longer read lengths, Pash 3.0 maps reads onto the large fraction of genomic DNA that contains repetitive elements and polymorphic sites, including indel polymorphisms.
  
  
  CONCLUSIONS
  We demonstrate the versatility of Pash 3.0 by analyzing the interaction between CpG methylation, CpG SNPs, and imprinting based on publicly available whole-genome shotgun bisulfite sequencing data. Pash 3.0 makes use of gapped k-mer alignment, a non-seed based comparison method, which is implemented using multi-positional hash tables. This allows Pash 3.0 to run on diverse hardware platforms, including individual computers with standard RAM capacity, multi-core hardware architectures and large clusters.
authors.affiliation: Department of Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza Houston, TX 77030, USA. coarfa@bcm.edu
authors.forename: Cristian
authors.initials: C
authors.lastname: Coarfa
authors.forename: Fuli
authors.initials: F
authors.lastname: Yu
authors.forename: Christopher A
authors.initials: CA
authors.lastname: Miller
authors.forename: Zuozhou
authors.initials: Z
authors.lastname: Chen
authors.forename: R Alan
authors.initials: RA
authors.lastname: Harris
authors.forename: Aleksandar
authors.initials: A
authors.lastname: Milosavljevic
mesh_terms: D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D030541:Databases, Genetic; D057890:Epigenomics / Q000379:methods*; D014644:Genetic Variation; D016678:Genome; D020641:Polymorphism, Single Nucleotide; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D004247:DNA