Genome-wide quantitative analysis of DNA methylation from bisulfite sequencing data

Bioinformatics. 2014 Jul 1;30(13):1933-4. doi: 10.1093/bioinformatics/btu142. Epub 2014 Mar 10.


Here we present the open-source R/Bioconductor software package BEAT (BS-Seq Epimutation Analysis Toolkit). It implements all bioinformatics steps required for the quantitative high-resolution analysis of DNA methylation patterns from bisulfite sequencing data, including the detection of regional epimutation events, i.e. loss or gain of DNA methylation at CG positions relative to a reference. Using a binomial mixture model, the BEAT package aggregates methylation counts per genomic position, thereby compensating for low coverage, incomplete conversion and sequencing errors.

Availability and implementation: BEAT is freely available as part of Bioconductor at The package is distributed under the GNU Lesser General Public License 3.0.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • DNA Methylation*
  • Genome
  • Genome-Wide Association Study
  • Genomics / methods*
  • High-Throughput Nucleotide Sequencing / methods*
  • Software Design
  • Sulfites / chemistry*


  • Sulfites