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In reduced representation bisulfite sequencing (RRBS), genomic DNA is digested with the restriction enzyme and then subjected to next‐generation sequencing, which enables detection and quantification of DNA methylation at whole‐genome scale with low cost. However, the data processing, interpretation, and analysis of the huge amounts of data generated pose a bioinformatics challenge. We developed RRBS‐Analyser, a comprehensive genome‐scale DNA methylation analysis server based on RRBS data. RRBS‐Analyser can assess sequencing quality, generate detailed statistical information, align the bisulfite‐treated short reads to reference genome, identify and annotate the methylcytosines (5mCs) and associate them with different genomic features in CG, CHG, and CHH content. RRBS‐Analyser supports detection, annotation, and visualization of differentially methylated regions (DMRs) for multiple …