BatMeth2

BatMeth2 is a software package for analyzing bisulfite sequencing (BS-Seq) data, which provides genome-wide DNA methylation levels at single-base resolution. The main features and improvements of BatMeth2 include:

1. Accurate alignment of BS reads while allowing for variable-length insertions and deletions (indels) relative to the reference genome, thus improving methylation calling accuracy, particularly in regions close to indels.

2. Calculate methylation levels for individual loci, genomic regions, or functional regions such as genes and transposable elements.

3. Additional programs for annotating methylation data, visualization, and detecting differentially methylated cytosines/regions (DMC/DMR).

4. User-friendly, autorun package that is easy to use and available as open-source software on GitHub.

Topic

Methylated DNA immunoprecipitation;Epigenetics;DNA

Detail

  • Operation: Whole genome methylation analysis;Gene methylation analysis;Bisulfite mapping

  • Software interface: Command-line tool,Library

  • Language: R

  • License: Not stated

  • Cost: Free of charge

  • Version name: -

  • Credit: The China Scholarship Council, the National Natural Science Foundation of China, the Fundamental Research Funds for the Central Universities.

  • Input: -

  • Output: -

  • Contact: Qiangwei Zhou qiangwei.zhou2013@gmail.com

  • Collection: -

  • Maturity: -

Publications

  • An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping.
  • Zhou Q, et al. An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping. An integrated package for bisulfite DNA methylation data analysis with Indel-sensitive mapping. 2019; 20:47. doi: 10.1186/s12859-018-2593-4
  • https://doi.org/10.1186/s12859-018-2593-4
  • PMID: 30669962
  • PMC: PMC6343306

Download and documentation

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