DNA methylation is a pervasive and important epigenetic regulator in mammalian genome. For DNA methylome profiling, emerging bisulfite-free methods have demonstrated desirable superiority over the conventional bisulfite-treatment-based approaches, although current analysis software could not make full use of their advantages. In this work, we present Msuite, an easy-to-use, all-in-one data-analysis toolkit. Msuite implements a unique 4-letter analysis mode specifically optimized for emerging protocols; it also integrates quality controls, methylation call, and data visualizations. Msuite demonstrates substantial performance improvements over current state-of-the-art tools as well as fruitful functionalities, thus holding the potential to serve as an optimal toolkit to facilitate DNA methylome studies. Source codes and testing datasets for Msuite are freely available at https://github.com/hellosunking/Msuite/.
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