We look at statistical methods to reduce error rates for Il-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.
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