The Polonator G.007 is a very flexible instrument, and can support a wide variety of sequencing protocols. For that matter, it is valuable for a number of non-sequencing-related biological applications. Its initial and primary application, however, is the efficient and highly automated implementation of the polony (polymerase colony) sequence by ligation protocol developed by the Church Laboratory. Prior to implementing this sequencing protocol, there are six upstream protocols required to prepare the DNA for sequencing.

The seven Polonator protocols are as follows: