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MethFlowVM: a virtual machine for the integral analysis of bisulfite sequencing data

Ricardo Lebrón, Guillermo Barturen, Cristina Gómez-Martín, José L. Oliver, Michael Hackenberg
doi: https://doi.org/10.1101/066795
Ricardo Lebrón
1Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
2Laboratorio de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, 18100-Granada. Spain
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Guillermo Barturen
3Genetics of Complex Diseases Group, GENyO. Pfizer-University of Granada-Junta de Andalucia Center for Genomics and Oncological Research
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Cristina Gómez-Martín
1Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
2Laboratorio de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, 18100-Granada. Spain
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José L. Oliver
1Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
2Laboratorio de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, 18100-Granada. Spain
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Michael Hackenberg
1Dpto. de Genética, Facultad de Ciencias, Universidad de Granada, Campus de Fuentenueva s/n, 18071-Granada, Spain
2Laboratorio de Bioinformática, Centro de Investigación Biomédica, PTS, Instituto de Biotecnología, Avda. del Conocimiento s/n, 18100-Granada. Spain
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Abstract

The analysis of whole genome DNA methylation patterns is an important first step towards the understanding on how DNA methylation is involved in the regulation of gene expression and genome stability.

Previously, we published MethylExtract, a program for DNA methylation profiling and genotyping from the same sample. Over the last years we developed it further into a methylation analysis pipeline that allows to take full advantage of novel genome assembly models. The result is a new pipeline termed MethFlow which permits both, profiling of methylation levels and differential methylation analysis.

Frequently DNA methylation research is carried out in the biomedical field, where privacy issues play an important role. Therefore we implemented the pipeline into a virtual machine termed MethFlowVM which shares with a web-server its user-friendliness however, the decisive advantage is that the sequencing data does not leave the user desktop or server and therefore no privacy issues do exist.

The virtual machine is available at: http://bioinfo2.uqr.es:8080/MethFlow/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-ND 4.0 International license.
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Posted July 31, 2016.
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MethFlowVM: a virtual machine for the integral analysis of bisulfite sequencing data
Ricardo Lebrón, Guillermo Barturen, Cristina Gómez-Martín, José L. Oliver, Michael Hackenberg
bioRxiv 066795; doi: https://doi.org/10.1101/066795
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MethFlowVM: a virtual machine for the integral analysis of bisulfite sequencing data
Ricardo Lebrón, Guillermo Barturen, Cristina Gómez-Martín, José L. Oliver, Michael Hackenberg
bioRxiv 066795; doi: https://doi.org/10.1101/066795

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