I will be performing direct sequencing of bisulfite PCR products (dye-terminator sequencing on the ABI 3730xl). I have come across many options for software in terms of base calling, quality control and normalisation of the sequencing traces. I know that ABI recommends KB Basecaller because it accounts for the skewed base composition in bisulfite converted product. Could anyone with experience recommend any other programs, specifically useful for methylation analyses? Thank you!