Which software/algorithm do you use to analyze methylation data

Question

[madkitty]

I'm curious to know what and how others are analyzing methylation data when looking at two set of samples (control vs. tumour). We have ERRBS methylation data (human samples) with replicates.

1. Which software / platform / pipeline do you use to analyze this kind of data?
2. Would you look for DMR?
3. Would you perform differential analysis?