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Enhanced Reduced Representation Bisulfite Sequencing for Assessment of DNA Methylation at Base Pair Resolution
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BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.

Weilong Guo, Petko Fiziev, Weihong Yan

  • 1Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, CA 90095, USA. paoyang@gate.sinica.edu.tw.

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Summary

BS-Seeker2 is a new pipeline for mapping bisulfite sequencing data to generate DNA methylomes. It accurately and efficiently analyzes both whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS) data.

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Area of Science:

  • Epigenetics
  • Genomics
  • Bioinformatics

Background:

  • DNA methylation is a key epigenetic modification regulating biological processes.
  • High-throughput sequencing, particularly whole genome bisulfite sequencing (WGBS) and reduced representation bisulfite sequencing (RRBS), enables base-resolution genome-wide DNA methylation studies.
  • Efficient and versatile alignment tools are crucial for processing bisulfite sequencing data.

Purpose of the Study:

  • To develop an updated and comprehensive pipeline for mapping bisulfite sequencing data.
  • To improve the efficiency and accuracy of DNA methylome generation.
  • To provide enhanced capabilities for analyzing both WGBS and RRBS libraries.

Main Methods:

  • Development of BS-Seeker2, an updated version of the BS Seeker pipeline.
  • Implementation of local alignment to improve read mappability.
  • Creation of specialized indexes for efficient and accurate mapping of RRBS reads.
  • Inclusion of a function to filter reads with incomplete bisulfite conversion.

Main Results:

  • BS-Seeker2 demonstrates improved mappability compared to existing aligners.
  • The pipeline efficiently and accurately maps reads from both WGBS and RRBS libraries.
  • BS-Seeker2 effectively minimizes the overestimation of DNA methylation levels by filtering incomplete conversion reads.
  • New CGmap and ATCGmap file formats were defined for comprehensive DNA methylome representation.

Conclusions:

  • BS-Seeker2 provides efficient and accurate performance for both WGBS and RRBS data analysis.
  • The pipeline is a valuable tool for generating DNA methylomes.
  • BS-Seeker2 is freely available for use.
  • The defined CGmap and ATCGmap formats offer enhanced DNA methylome representations.