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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution

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gemBS: high throughput processing for DNA methylation data from bisulfite sequencing.

Angelika Merkel1, Marcos Fernández-Callejo1, Eloi Casals1

  • 1Centro Nacional de Análisis Genómico (CNAG-CRG), Centre de Regulacio Genómico (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain.

Bioinformatics (Oxford, England)
|August 24, 2018
PubMed
Summary
This summary is machine-generated.

We developed gemBS, a fast bioinformatics pipeline for analyzing whole genome bisulfite sequencing (WGBS) data. This tool efficiently handles large datasets, providing accurate methylation estimates and genotype information for mammalian development studies.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Epigenetics

Background:

  • DNA methylation is crucial for mammalian embryogenesis and development.
  • Whole genome bisulfite sequencing (WGBS) captures DNA methylation at single base pair resolution.
  • Existing WGBS analysis tools struggle with the large data volumes generated by modern studies.

Purpose of the Study:

  • To develop a fast, high-throughput bioinformatics pipeline for large-scale BS-Seq analysis.
  • To address the limitations of current tools in terms of functionality and efficiency.
  • To enable comprehensive and reproducible analysis of WGBS data.

Main Methods:

  • Developed gemBS, a bioinformatics pipeline integrating a high-performance BS-mapper (GEM3) and a BS-Seq variant caller (BScall).
  • Designed gemBS for efficient processing of large-scale bisulfite sequencing data.
  • Incorporated modularity for automation and ease of use.

Main Results:

  • gemBS provides genotype information and methylation estimates for all genomic cytosines (CpG and non-CpG contexts).
  • The pipeline generates quality reports for comprehensive and reproducible analysis.
  • gemBS demonstrates robust and accurate results, handling large datasets efficiently.

Conclusions:

  • gemBS offers a powerful and efficient solution for large-scale whole genome bisulfite sequencing analysis.
  • The pipeline facilitates accurate methylation and genotype calling, essential for developmental studies.
  • gemBS is modular, automatable, and provides reproducible results for the research community.