metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
- Frank Jühling,
- Helene Kretzmer,
- Stephan H. Bernhart,
- Christian Otto,
- Peter F. Stadler and
- Steve Hoffmann1
- ↵* Corresponding author; email: steve{at}bioinf.uni-leipzig.de
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 sequencing data with unrivaled specificity and sensitivity. A binary segmentation algorithm combined with a two-dimensional statistical test allows to detect DMRs in large methylation experiments with multiple groups of samples in minutes rather than days using off-the-shelf hardware. metilene outperforms other state-if-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 samples per group, or even without biological replicates, it produces highly significant and reliable results.
- Received July 1, 2015.
- Accepted November 25, 2015.
- Published by Cold Spring Harbor Laboratory Press
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