ME-plot: A QC package for bisulfite sequencing reads

Abstract

Summary: Bisulfite sequencing is the gold standard method for analyzing methylomes. However, the effect of quality control in bisulfite sequencing has not been studied extensively. We developed a package ME-Plot to detect the errors in bisulfite sequencing mapping data and produce higher quality methylation calls by trimming low quality portions of the reads. Our simulation results on both randomly generated reads where methylation status is known and real world data indicate that ME-plot can detect errors in methylation mapping procedures and suggest post-processing steps to reduce the errors. ME-Plot requires SAM/BAM files for its analysis. Availability: The python package is available at the following URL. https://github.com/joshuabhk/methylsuite