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ViewBS: a powerful toolkit for visualization of high-throughput bisulfite sequencing data.

Xiaosan Huang1, Shaoling Zhang1, Kongqing Li2

  • 1College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, No.6 Tongwei Road Nanjing, P. R. China, 210095.

Bioinformatics (Oxford, England)
|November 1, 2017
PubMed
Summary

ViewBS is an open-source toolkit that simplifies DNA methylome data visualization from bisulfite sequencing (BS-seq). It generates publication-quality figures for plant and animal research, accelerating biological discovery.

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Area of Science:

  • Genomics
  • Bioinformatics
  • Epigenetics

Background:

  • High-throughput bisulfite sequencing (BS-seq) is crucial for single-base DNA methylome analysis in diverse organisms.
  • Accelerating BS-seq data analysis necessitates efficient visualization tools.

Purpose of the Study:

  • To introduce ViewBS, an open-source toolkit designed for easy and flexible extraction and visualization of DNA methylome data.
  • To enable rapid visualization of large BS-seq datasets using Tabix integration.
  • To facilitate the generation of publication-quality figures for biological interpretation.

Main Methods:

  • Development of the ViewBS open-source toolkit.
  • Integration of Tabix for efficient handling of large BS-seq datasets.
  • Implementation of visualization modules for meta-plots, heat maps, and violin-boxplots.

Main Results:

  • ViewBS provides a flexible and user-friendly interface for BS-seq data visualization.
  • The toolkit enables rapid processing of large datasets, significantly speeding up analysis.
  • Publication-quality figures, including meta-plots, heat maps, and violin-boxplots, can be generated.
  • Successful application demonstrated using Arabidopsis thaliana BS-seq data.

Conclusions:

  • ViewBS is a valuable open-source tool for accelerating DNA methylome data analysis and visualization.
  • The toolkit aids researchers in answering complex biological questions through clear data representation.
  • ViewBS enhances the utility of BS-seq technology in plant and animal epigenetics research.