Extracts and analyzes the epihaplotype composition of reads from targeted bisulfite sequencing experiments. ampliMethProfiler is a python-based pipeline for the extraction and statistical epihaplotype analysis of amplicons from targeted deep bisulfite sequencing of multiple DNA regions. This tool can be used for the extraction and analysis of methylation profiles at the single molecule level from deep targeted bisulfite sequencing of multiple DNA regions.

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ampliMethProfiler specifications

Software type:
Pipeline
Restrictions to use:
None
Input format:
FASTA
Programming languages:
Python
Computer skills:
Advanced
Stability:
Beta
Interface:
Command line interface
Input data:
Requires three types of input files: a file containing the reads from the sequencer in FASTA format, a comma-separated file containing information on the sequenced regions, and a FASTA file containing the reference sequences of the analyzed regions.
Operating system:
Unix/Linux, Mac OS
License:
GNU General Public License version 3.0
Version:
1.1
Requirements:
Biom v. 2.1.5+, QIIME v. 1.9+, Biopython v. 1.65+, Blast v. 2.2.25+.

Publications

  • (Scala et al., 2016) ampliMethProfiler: a pipeline for the analysis of CpG methylation profiles of targeted deep bisulfite sequenced amplicons. BMC Bioinformatics.
    PMID: 27884103

ampliMethProfiler support

Documentation

Credits

Institution(s)

Istituto Nazionale di Fisica Nucleare, Sezione di Napoli, Naples, Italy; 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; Dipartimento di Fisica, Università degli Studi di Napoli "Federico II", Naples, Italy

Funding source(s)

This work was supported by the Doctorate of Computational Biology and Bioinformatics, University “Federico II”, Naples and partially supported by the Epigenomic Flagship Project-Epigen, Research Council of Italy (CNR); and the POR Campania FSE 2007–2013, Project CREME.

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