The codes contain the basic processes for WGBS analysis, which contain QC, mapping, and differential analysis. Automatic pipeline and large samples should be considered in the future.
- Quality control: FastQC, Trim_Galore
- The major mapping software used: Bismark
- Other mapping softwares: BSMAP, Bwameth, WALT. Some comparison between Bismark and BSMAP in Chinese could be found here.
- Differentially methylated analysis: methylKit, MethPipe, metilene, Comb-p
- Allele-specific methylation: MethPipe
- SNP calling: Bis-SNP
- Annotation: methylKit and customized strategy.
