Can tracy's consensus option be updated?

[zahidul-islam-nahid]

I am using Tracy to generate consensus, and then the mutations are being analysed using Mummer. But when I was comparing the result with the Pearl (online) of the gear-genomics, some mutations were not seen. I traced the problem back to the base-calling. So, if it is possible to update the algorithm of Tracy to that of Pearl for base-calling, it will be great.

It is just my observation. I am not an expert. Excuse me if I am wrong.