metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
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.
Jühling, Frank and Kretzmer, Helene and Bernhart, Stephan H and Otto, Christian and Stadler, Peter F and Hoffmann, Steve: 'metilene: Fast and sensitive calling of differentially methylated regions from bisulfite sequencing data', Published in Advance, Genome Research, 2015.