BisSeq: a reduced representation bisulfite sequencing simulation and analysis tool

Abstract

Reduced representation bisulfite sequencing is gaining popularity among researchers who focus on epigenetics. But with an ever-increasing availability of downstream mapping software, no clear standard has been established, hence impairing confidence of experimental results. Simulation of NGS data coupled with software performance analysis provides an alternative way. BisSeq is a new next-generation sequencing simulator capable of generating single-end reduced representation bisulfite sequencing reads in FASTA format. BisSeq allows users to configure different sequencing parameters, facilitating various research purposes. BisSeq integrates data visualization methods to help researchers assess the performance of sequencing read aligners after bisulfite conversion of cytosine’s to thymidines. Currently BisSeq supports simulation against single genome. We demonstrate BisSeq's value by using Bismark to map simulated sequencing reads. Working with reads simulated with different read length; we profiled performance of BSseeker2, BSMAP, Bismark using a comparison metric. BisSeq provides researchers with a good tool to benchmark reads mapping tools and to identify appropriate parameter values for experimental design.