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

ABSTRACT: Motivation:High throughput bisulfite sequencing (BS-seq) is an important technology to generate single-base DNA methylomes in both plants and animals. In order to accelerate the data analysis of BS-seq data, toolkits for visualization are required. Results:ViewBS, an open-source toolkit, can extract and visualize the DNA methylome data easily and with flexibility. By using Tabix, ViewBS can visualize BS-seq for large datasets quickly. ViewBS can generate publication-quality figures, such as meta-plots, heat maps and violin-boxplots, which can help users to answer biological questions. We illustrate its application using BS-seq data from Arabidopsis thaliana. Availability:ViewBS is freely available at: https://github.com/xie186/ViewBS. Contact:xie186@purdue.edu. Supplementary information:Supplementary data are available at Bioinformatics online.

SUBMITTER: Huang X

PROVIDER: S-EPMC5860610 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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

Huang Xiaosan X Zhang Shaoling S Li Kongqing K Thimmapuram Jyothi J Xie Shaojun S Wren Jonathan J

Bioinformatics (Oxford, England) 20180201 4

<h4>Motivation</h4>High throughput bisulfite sequencing (BS-seq) is an important technology to generate single-base DNA methylomes in both plants and animals. In order to accelerate the data analysis of BS-seq data, toolkits for visualization are required.<h4>Results</h4>ViewBS, an open-source toolkit, can extract and visualize the DNA methylome data easily and with flexibility. By using Tabix, ViewBS can visualize BS-seq for large datasets quickly. ViewBS can generate publication-quality figure ...[more]

PMID: 29087450

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Project description:BackgroundBisulfite sequencing is one of the most widely used technologies in analyzing DNA methylation patterns, which are important in understanding and characterizing the mechanism of DNA methylation and its functions in disease development. Efficient and user-friendly tools are critical in carrying out such analysis on high-throughput bisulfite sequencing data. However, existing tools are either not scalable well, or inadequate in providing visualization and other desirable functionalities.ResultsIn order to handle ultra large sequencing data and to provide additional functions and features, we have developed BSPAT, a fast online tool for bisulfite sequencing pattern analysis. With a user-friendly web interface, BSPAT seamlessly integrates read mapping/quality control/methylation calling with methylation pattern generation and visualization. BSPAT has the following important features: 1) instead of using multiple/pairwise sequence alignment methods, BSPAT adopts an efficient and widely used sequence mapping tool to provide fast alignment of sequence reads; 2) BSPAT summarizes and visualizes DNA methylation co-occurrence patterns at a single nucleotide level, which provide valuable information in understanding the mechanism and regulation of DNA methylation; 3) based on methylation co-occurrence patterns, BSPAT can automatically detect potential allele-specific methylation (ASM) patterns, which can greatly enhance the detection and analysis of ASM patterns; 4) by linking directly with other popular databases and tools, BSPAT allows users to perform integrative analysis of methylation patterns with other genomic features together within regions of interest.ConclusionBy utilizing a real bisulfite sequencing dataset generated from prostate cancer cell lines, we have shown that BSPAT is highly efficient. It has also reported some interesting methylation co-occurrence patterns and a potential allele-specific methylation case. In conclusion, BSPAT is an efficient and convenient tool for high-throughput bisulfite sequencing data analysis that can be broadly used.

Dataset Information

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

Publications

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

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