Recommendation list

Bismark base multi sample comparison pipeline(PE, with RefFlat annotation)
Bismark base multi sample comparison pipeline(SE, with RefFlat annotation)
BMap base multi sample comparison pipeline (PE)
BMap base multi sample comparison pipeline (SE)

Related list

Bismark (SE)
Bismark (PE)
FastQC (SE)

Note "SE": For single-end read, "PE": For paired-end read, "GE": Genome explorer which is our original genome browser.
It is necessary to register to analyze your own data.
: The popular pipeline or the latest one that the developer recommend.
Notice: Unrecomend not a tool used by the pipeline but the workflow of the pipelie.

References:

• Nat Methods. 2012 Jan 30;9(2):145-51. doi: 10.1038/nmeth.1828.