Figure 1
From: ParticleCall: A particle filter for base calling in next-generation sequencing systems

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 and λ t , which represent a subsequence of the template centered at position t and per-cluster density, respectively.