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Simulates genetic variations that are divergent from reference sequence along with the sequencing error and quality distributions. BSSim is a BS-seq simulator that provides output read datasets for Illumina's Solexa, Roche's 454 and Applied Biosystems' SOLiD. It allows users to mimic various methylation level (total methylation level of cytosines, percentage of cytosines that methylated and methylation level of total methylcytosines) and bisulfite conversion rate in CpG, CHG and CHH context.