Base calling error rates in next-generation DNA sequencing

Manohar Shamaiah, Haris Vikalo

Abstract: We study the problem of base calling in next-generation DNA sequencing platforms that rely on reversible terminator chemistry. After reviewing a statistical model of the generated signal and the Viterbi algorithm for finding the maximum-likelihood solution to the base calling problem, we present a closed form expression for the upper bound on the probability of base calling error. Simulation results demonstrate that the derived upper bound provides a useful characterization of the error rate performance of the considered sequencing platform.