BAT

BAT (Bisulfite Analysis Toolkit) is a software tool to analyze DNA methylation using bisulfite sequencing data. The BAT package includes modules that users can customize or extend:
Mapping module. Includes pre- and postprocessing.
Calling module to extract methylation information from alignments.
Analysis module up to multiple samples.
DMR calling module inludes basic statistics and expression information, histone modification data, and transcription factor binding data.

Topic

Sequence analysis

Detail

  • Operation: Sequence analysis;Mapping;Variant calling;Sequence annotation;Bisulfite mapping

  • Software interface: Script;Workflow;Suite

  • Language: R;Shell;Perl

  • License: The MIT licence

  • Cost: Free

  • Version name: 0.1

  • Credit: German BMBF, ICGC-Data Mining, the European Union in the framework of the BLUEPRINT Project and LIFE (Leipzig Research Center for Civilization Diseases), Leipzig University, the European Regional Development Fund (ERDF), the European Social Fund (ESF), the Free State of Saxony within the excellence initiative, German Research Foundation (DFG).

  • Input: -

  • Output: -

  • Contact: helene@bioinf.uni-leipzig.de

  • Collection: -

  • Maturity: Emerging

Publications

  • BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs.
  • Kretzmer H, Otto C, Hoffmann S. BAT: Bisulfite Analysis Toolkit: BAT is a toolkit to analyze DNA methylation sequencing data accurately and reproducibly. It covers standard processing and analysis steps from raw read mapping up to annotation data integration and calculation of correlating DMRs. F1000Res. 2017 Aug 16;6:1490. doi: 10.12688/f1000research.12302.1. PMID: 28979767; PMCID: PMC5590080.
  • https://doi.org/10.12688/f1000research.12302.1
  • PMID: 28979767
  • PMC: PMC5590080

Download and documentation

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