Figure 1

A hidden Markov model of the generated signal in Illumina sequencing-by-synthesis platforms. An illustration of the graphical HMM of the Illumina’s sequencing platform. The observations ^y″represent signal intensities after the removal of residual effects. The states are the combinations of $S_t^w$ and _{λ t} , which represent a subsequence of the template centered at position t and per-cluster density, respectively.