Deoxynucleotide triphosphates (dNTPs) are flowed over the surface of the bead in a predetermined sequence, with zero or more dNTPs ligating during each flow. While the first generation of the PGM cycled through the four nucleotides in a step-wise fashion (as does the Roche 454 pyrosequencer), this cycle was modified to have a period of 32, with a pattern that repeats some nucleotides in a period shorter than four. This more complex flow cycle, referred to as the Samba, was implemented to improve synchronicity of clonal templates on the bead at the cost of a flow-sequence not optimised for read length. A single proton is released for every nucleotide incorporated during the flow, resulting in a net decrease of the pH in the surrounding solution. This pH change is measured by an ionic sensor and then converted to a flow value using a physical model of the cell and its contents. The PGM base-caller takes these flow-values and corrects for phase and signal loss, and also normalizes the raw flow-values to the key sequence (the key is a known four-base
