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

BMC Bioinformatics

Table 1 Comparison of ParticleCall with different _{N
p}

Method	_{N p}	error rate	base-calling time (min)
ParticleCall (via MCEM)	400	0.0126	46
	800	0.0124	88
	1200	0.0124	130
ParticleCall (via PFEM)	400	0.0128	46
	800	0.0125	91
	1200	0.0125	133
Rao-Blackwellized ParticleCall (via MCEM)	100	0.0128	103
	200	0.0125	190
	300	0.0124	287
	400	0.0124	386

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. Rao-Blackwellized ParticleCall is run using parameters via the MCEM parameter estimation scheme.

ISSN: 1471-2105