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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

ParticleCall

   

(via MCEM)

0.0124

88

1139

ParticleCall

   

(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.
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BMC Bioinformatics

ISSN: 1471-2105

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