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

Genome Res. 2016 Feb;26(2):256-62. doi: 10.1101/gr.196394.115. Epub 2015 Dec 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 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Case-Control Studies
  • Cerebellar Neoplasms / genetics
  • CpG Islands
  • DNA Methylation*
  • Humans
  • Medulloblastoma / genetics
  • Sequence Analysis, DNA*
  • Software*