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Metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.

ABSTRACT: The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs within whole-genome and targeted data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows the detection of DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardware. metilene outperforms other state-of-the-art tools for low coverage data and can estimate missing data. Hence, metilene is a versatile tool to study the effect of epigenetic modifications in differentiation/development, tumorigenesis, and systems biology on a global, genome-wide level. Whether in the framework of international consortia with dozens of samples per group, or even without biological replicates, it produces highly significant and reliable results.

SUBMITTER: Juhling F 

PROVIDER: S-EPMC4728377 | biostudies-literature | 2016 Feb

REPOSITORIES: biostudies-literature

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metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data.

Jühling Frank F   Kretzmer Helene H   Bernhart Stephan H SH   Otto Christian C   Stadler Peter F PF   Hoffmann Steve S  

Genome research 20151202 2

The detection of differentially methylated regions (DMRs) is a necessary prerequisite for characterizing different epigenetic states. We present a novel program, metilene, to identify DMRs within whole-genome and targeted data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows the detection of DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardwa  ...[more]

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