MethyMer
Design of specific primer combinations for bisulfite sequencing
...These regions are difficult in terms of selection appropriate primers because of their low-complexity, polyN-, CG-richness, etc.
MethyMer have a flexible scoring system capable of selecting primers in problematic regions (e.g. SpG islands) and includes specificity test (based on bowtie alignment against bisulfite-treated genome).
It also incorporates TCGA CpG methylation (microarrays) and gene expression (RNA-Seq) data, as well as methylation-expression correlation analysis results for 20 human cancer types.
ENCODE genome regions annotation data are also integrated in MethyMer