VAliBS: A visual aligner for bisulfite sequences

Abstract

Background: Methylation is a common modification of DNA. It has been a very important and hot topic to study the correlation between methylation and diseases in medical science. Because of the special process with bisulfite treatment, traditional mapping tools do not work well with such methylation experimental reads. Traditional aligners are not designed for mapping bisulfite-treated reads, where the un-methylated 'C's are converted to 'T's. Results: In this paper, we develop a reliable and visual tool, named VAliBS, for mapping bisulfate sequences to a genome reference. VAliBS works well even on large scale data or high noise data. By comparing with other state-of-the-art tools (BisMark, BSMAP, BS-Seeker2), VAliBS can improve the accuracy of bisulfite mapping. Moreover, VAliBS is a visual tool which makes its operations more easily and the alignment results are shown with colored marks which makes it easier to be read. VAliBS provides fast and accurate mapping of bisulfite-converted reads, and a friendly window system to visualize the detail of mapping of each read. Conclusions: VAliBS works well on both simulated data and real data. It can be useful in DNA methylation research. VALiBS implements an X-Window user interface where the methylation positions are visual and the operations are friendly.