BSviewer: a genotype-preserving, nucleotide-level visualizer for bisulfite sequencing data

Abstract

Motivation: The bisulfite sequencing technology has been widely used to study the DNA methylation profile in many species. However, most of the current visualization tools for bisulfite sequencing data only provide high-level views (i.e. overall methylation densities) while miss the methylation dynamics at nucleotide level. Meanwhile, they also focus on CpG sites while omit other information (such as genotypes on SNP sites) which could be helpful for interpreting the methylation pattern of the data. A bioinformatics tool that visualizes the methylation statuses at nucleotide level and preserves the most essential information of the sequencing data is thus valuable and needed. Results: We have developed BSviewer, a lightweight nucleotide-level visualization tool for bisulfite sequencing data. Using an imprinting gene as an example, we show that BSviewer could be specifically helpful for interpreting the data with allele-specific DNA methylation pattern. Availability and implementation: BSviewer is implemented in Perl and runs on most GNU/Linux platforms. Source code and testing dataset are freely available at http://sunlab.cpy.cuhk.edu.hk/BSviewer/. Contact: haosun@cuhk.edu.hk.