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Table 3 Comparison of error rates and speed

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

   base-calling parameter estimation
Method error rate time (min) time (min)
Bustard 0.0152 2 (total)  
Rolexa 0.0170 35 (total)  
naiveBayesCall 0.0132 21 1139
BayesCall 0.0124 231 1139
(via MCEM) 0.0124 88 1139
(via PFEM) 0.0125 91 39
  1. The base-calling error rate and the running times of different algorithms. ParticleCall is run using parameters obtained via the MCEM parameter estimation scheme as well as via the PFEM parameter estimation algorithm proposed in this paper. For Bustard and Rolexa, only the total running times are reported.