An MCMC algorithm for base calling in sequencing-by-synthesis

Sequencing-by-synthesis is a novel technology which enables fast and affordable DNA sequencing. However, its accuracy is insufficient for most medical applications. The performance of sequencing-by-synthesis is fundamentally limited by imperfections in the underlying enzymatic process. We derive a mathematical model of sequencing-by-synthesis and develop a novel base calling method that relies on Markov Chain Monte Carlo technique. Simulation and experimental results demonstrate superior performance of the proposed method over the state-of-the-art base-calling techniques.