A new parallel pipeline for DNA methylation analysis of long reads datasets.

TitleA new parallel pipeline for DNA methylation analysis of long reads datasets.
Publication TypeJournal Article
Year of Publication2017
AuthorsOlanda R, Pérez M, Orduña JM, Tárraga J, Dopazo J
Journal TitleBMC bioinformatics
Volume18
Pages161
Journal Date2017 Mar 09
ISSN1471-2105
KeywordsMethyl-Seq, NGS
AbstractBACKGROUND: DNA methylation is an important mechanism of epigenetic regulation in development and disease. New generation sequencers allow genome-wide measurements of the methylation status by reading short stretches of the DNA sequence (Methyl-seq). Several software tools for methylation analysis have been proposed over recent years. However, the current trend is that the new sequencers and the ones expected for an upcoming future yield sequences of increasing length, making these software tools inefficient and obsolete. RESULTS: In this paper, we propose a new software based on a strategy for methylation analysis of Methyl-seq sequencing data that requires much shorter execution times while yielding a better level of sensitivity, particularly for datasets composed of long reads. This strategy can be exported to other methylation, DNA and RNA analysis tools. CONCLUSIONS: The developed software tool achieves execution times one order of magnitude shorter than the existing tools, while yielding equal sensitivity for short reads and even better sensitivity for long reads.
URLhttp://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1574-3
DOI10.1186/s12859-017-1574-3
Alternate JournalBMC Bioinformatics