BMC Bioinformatics

Table 1 Simulation study alignment statistics using optimal model parameters

From: Clinical PathoScope: rapid alignment and filtration for accurate pathogen identification in clinical samples using unassembled sequencing data

	Human		Virus		Bacteria
	Time (m)	Sensitivity	Time (m)	Sensitivity	Time (m)	Sensitivity
	Time (m)	Specificity	Time (m)	Specificity	Time (m)	Specificity
Bowtie2	8.2 ± 0.0	90.2 ± 0.0	3.3 ± 0.6	98 .1 ± 0.6	15.8 ± 1.6	79.8 ± 0.1
Bowtie2	8.2 ± 0.0	100.0 ± 0.0	3.3 ± 0.6	99.8 ± 0.2	15.8 ± 1.6	100.0 ± 0.0
BWA	22.8 ± 3.2	89.9 ± 0.0	6.5 ± 1.4	76.8 ± 5.4	-	-
BWA	22.8 ± 3.2	100.0 ± 0.0	6.5 ± 1.4	99.8 ± 0.2	-	-
SOAP2	5.7 ± 1.6	76.7 ± 0.0	3.9 ± 0.8	50.3 ± 5.4	23.3 ± 2.2	27.7 ± 0.0
SOAP2	5.7 ± 1.6	100.0 ± 0.0	3.9 ± 0.8	99.9 ± 0.1	23.3 ± 2.2	100 ± 0.0
PBLAT	61.2 ± 6.8	78.2 ± 0.0	16.7 ± 1.3	99.8 ± 0.1	306.3 ± 23.3	98.9 ± 0.0
PBLAT	61.2 ± 6.8	100.0 ± 0.0	16.7 ± 1.3	99.6 ± 0.2	306.3 ± 23.3	52.7 ± 0.0

Each aligner was used to align the first set of five simulated sequencing samples (10 million 100 base-pair reads) against each of the three genome libraries using optimal parameters. The average run time, sensitivity, and specificity as well as confidence intervals for each alignment are reported. BWA failed to run to completion with the bacterial library.

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