BSeQC: quality control of bisulfite sequencing experiments

Bioinformatics. 2013 Dec 15;29(24):3227-9. doi: 10.1093/bioinformatics/btt548. Epub 2013 Sep 23.


Motivation: Bisulfite sequencing (BS-seq) has emerged as the gold standard to study genome-wide DNA methylation at single-nucleotide resolution. Quality control (QC) is a critical step in the analysis pipeline to ensure that BS-seq data are of high quality and suitable for subsequent analysis. Although several QC tools are available for next-generation sequencing data, most of them were not designed to handle QC issues specific to BS-seq protocols. Therefore, there is a strong need for a dedicated QC tool to evaluate and remove potential technical biases in BS-seq experiments.

Results: We developed a package named BSeQC to comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases that may result in inaccurate methylation estimation. BSeQC takes standard SAM/BAM files as input and generates bias-free SAM/BAM files for downstream analysis. Evaluation based on real BS-seq data indicates that the use of the bias-free SAM/BAM file substantially improves the quantification of methylation level.

Availability and implementation: BSeQC is freely available at:

Publication types

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

MeSH terms

  • Animals
  • DNA Methylation*
  • Databases, Factual
  • Embryonic Stem Cells / metabolism
  • Genome
  • High-Throughput Nucleotide Sequencing*
  • Humans
  • Mice
  • Neurons / metabolism
  • Quality Control*
  • Software*
  • Stem Cells / metabolism
  • Sulfites / chemistry*


  • Sulfites
  • hydrogen sulfite