title: ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons.
abstract: BACKGROUND
  CpG sites in an individual molecule may exist in a binary state (methylated or unmethylated) and each individual DNA molecule, containing a certain number of CpGs, is a combination of these states defining an epihaplotype. Classic quantification based approaches to study DNA methylation are intrinsically unable to fully represent the complexity of the underlying methylation substrate. Epihaplotype based approaches, on the other hand, allow methylation profiles of cell populations to be studied at the single molecule level. For such investigations, next-generation sequencing techniques can be used, both for quantitative and for epihaplotype analysis. Currently available tools for methylation analysis lack output formats that explicitly report CpG methylation profiles at the single molecule level and that have suited statistical tools for their interpretation.
  
  
  RESULTS
  Here we present ampliMethProfiler, a python-based pipeline for the extraction and statistical epihaplotype analysis of amplicons from targeted deep bisulfite sequencing of multiple DNA regions.
  
  
  CONCLUSIONS
  ampliMethProfiler tool provides an easy and user friendly way to extract and analyze the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is written in python language and requires a local installation of BLAST and (optionally) QIIME tools. It can be run on Linux and OS X platforms. The software is open source and freely available at http://amplimethprofiler.sourceforge.net .
authors.affiliation: Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy. gscala@na.infn.it.
authors.forename: Giovanni
authors.identifier: http://orcid.org/0000-0002-9619-9426
authors.initials: G
authors.lastname: Scala
authors.affiliation: Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy.|Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore", Consiglio Nazionale delle Ricerche CNR, Naples, Italy.
authors.forename: Ornella
authors.initials: O
authors.lastname: Affinito
authors.affiliation: Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy.
authors.forename: Domenico
authors.initials: D
authors.lastname: Palumbo
authors.affiliation: Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy.|Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore", Consiglio Nazionale delle Ricerche CNR, Naples, Italy.
authors.forename: Ermanno
authors.initials: E
authors.lastname: Florio
authors.affiliation: Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore", Consiglio Nazionale delle Ricerche CNR, Naples, Italy.
authors.forename: Antonella
authors.initials: A
authors.lastname: Monticelli
authors.affiliation: Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy.|Dipartimento di Fisica, Università degli Studi di Napoli "Federico II", Naples, Italy.
authors.forename: Gennaro
authors.initials: G
authors.lastname: Miele
authors.affiliation: Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy.|Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore", Consiglio Nazionale delle Ricerche CNR, Naples, Italy.
authors.forename: Lorenzo
authors.initials: L
authors.lastname: Chiariotti
authors.affiliation: Dipartimento di Medicina Molecolare e Biotecnologie Mediche, Università degli Studi di Napoli "Federico II", Naples, Italy.|Istituto di Endocrinologia ed Oncologia Sperimentale (IEOS) "Gaetano Salvatore", Consiglio Nazionale delle Ricerche CNR, Naples, Italy.
authors.forename: Sergio
authors.initials: S
authors.lastname: Cocozza
mesh_terms: D000818:Animals; D018899:CpG Islands / Q000235:genetics*; D050804:D-Aspartate Oxidase / Q000235:genetics*; D004247:DNA / Q000032:analysis / Q000737:chemistry* / Q000235:genetics; D019175:DNA Methylation; D041981:Gastrointestinal Tract / Q000378:metabolism; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D051379:Mice; D017422:Sequence Analysis, DNA / Q000379:methods; D012984:Software; D013447:Sulfites / Q000737:chemistry
chemical_list: D013447:Sulfites; D004247:DNA; D050804:D-Aspartate Oxidase; C042345:hydrogen sulfite
keywords: Bisulfite sequencing; DNA methylation; Epihaplotype; Epihaplotype based analysis; Methylation profiles