title: PASS-bis: a bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads.
abstract: CONCLUSIONS
  The sequencing of bisulfite-treated DNA (Bi-Seq) is becoming a gold standard for methylation studies. The mapping of Bi-Seq reads is complex and requires special alignment algorithms. This problem is particularly relevant for SOLiD color space, where the bisulfite conversion C/T changes two adjacent colors into 16 possible combinations. Here, we present an algorithm that efficiently aligns Bi-Seq reads obtained either from SOLiD or Illumina. An accompanying methylation-caller program creates a genomic view of methylated and unmethylated Cs on both DNA strands.
  
  
  METHODS
  The algorithm has been implemented as an option of the program PASS, freely available at http://pass.cribi.unipd.it.
  
  
  BACKGROUND
  pass@cribi.unipd.it
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: CRIBI Biotechnology Centre, Università di Padova, 35131 Padova, Italy.
authors.forename: Davide
authors.initials: D
authors.lastname: Campagna
authors.forename: Andrea
authors.initials: A
authors.lastname: Telatin
authors.forename: Claudio
authors.initials: C
authors.lastname: Forcato
authors.forename: Nicola
authors.initials: N
authors.lastname: Vitulo
authors.forename: Giorgio
authors.initials: G
authors.lastname: Valle
mesh_terms: D000465:Algorithms; D003116:Color; D019175:DNA Methylation; D023281:Genomics; D006801:Humans; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D013447:Sulfites
chemical_list: D013447:Sulfites; C042345:hydrogen sulfite