Base-calling for Illumina´s next-generation DNA sequencing systems via Viterbi algorithm

We look at statistical methods to reduce error rates for II lumina´s next-generation sequencing platforms. In particular, we propose a computationally tractable parametric model for Illumina´s Genome Analyzer which is amenable to the use of dynamic programming ideas. We investigate the performance of the proposed algorithm for base-calling in terms of error rates, compare it with the state-of-the-art basecalling schemes for this platform, and demonstrate its feasibility on experimentally obtained data.