ampliMethProfiler statistics

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Number of citations per year for the bioinformatics software tool ampliMethProfiler
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ampliMethProfiler specifications

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Unique identifier OMICS_13845
Name ampliMethProfiler
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
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.
Input format FASTA
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.1
Stability Beta
Requirements
Biom, QIIME, BioPython, Blast
Maintained Yes

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Publication for ampliMethProfiler

ampliMethProfiler citations

 (3)
library_books

High coverage methylation data of a gene model before and after DNA damage and homologous repair

2017
Sci Data
PMCID: 5387920
PMID: 28398335
DOI: 10.1038/sdata.2017.43

[…] rted into that of the (+) strand and pooled together with the original (+) strand. The four files analysed correspond to the (+) strand.To analyse the methylation status of each amplicon, we used the AMPLIMETHPROFILER specifically designed for deep-targeted bisulfite amplicon sequencing of multiple genomic regions. This pipeline is freely available at https://sourceforge.net/projects/amplimethprof […]

library_books

Non homologous end joining induced alterations in DNA methylation: A source of permanent epigenetic change

2017
Oncotarget
PMCID: 5522286
PMID: 28423717
DOI: 10.18632/oncotarget.16122

[…] of 40 overlapping residues as threshold (mean PHREAD score of at least 33) and merged FastQ files were converted in Fasta using Prinseq. [] To analyze the methylation status of each amplicon, we used AMPLIMETHPROFILER [] specifically designed for deep targeted bisulfite amplicon sequencing of multiple genomic regions. This pipeline is freely available at https://sourceforge.net/projects/amplimethp […]

library_books

Tracking the evolution of epialleles during neural differentiation and brain development: D Aspartate oxidase as a model gene

2016
Epigenetics
PMCID: 5270635
PMID: 27858532
DOI: 10.1080/15592294.2016.1260211

[…] reshold a mean PHREAD score of at least 33. FASTQ assembled reads were converted to FASTA format using PRINSEQ tool. To analyze the methylation status of each amplicon, we used our pipeline software (Amplimethprofiler), freely available at https://sourceforge.net/projects/amplimethprofiler. This tool is specifically designed for deep targeted bisulfite amplicon sequencing of multiple genomic regio […]


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ampliMethProfiler 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
ampliMethProfiler 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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