BMC Bioinformatics

Table 1 Analysis of single-end data simulated with ART

From: Adaptable probabilistic mapping of short reads using position specific scoring matrices

		Unfiltered		MapQ filtered
	Mapper	Sensitivity	PPV	Sensitivity	PPV	Time (s)
a) ART single-end length 36
	BWA-PSSM	0.811	0.899	0.776	1.000	44.19
	BWA	0.804	0.896	0.735	1.000	47.41
	BWA-MEM	0.772	0.900	0.663	1.000	146.99
	Bowtie	0.812	0.900	*	*	9.75
	Bowtie2	0.802	0.898	0.757	0.999	28.67
	GEM	0.755	0.995	*	*	34.57
b) ART single-end length 50
	BWA-PSSM	0.839	0.934	0.797	0.999	96.07
	BWA	0.805	0.929	0.753	0.999	84.65
	BWA-MEM	0.816	0.921	0.719	1.000	56.64
	Bowtie	0.840	0.931	*	*	15.74
	Bowtie2	0.802	0.918	0.717	0.999	48.58
	GEM	0.705	0.995	*	*	35.45
c) ART single-end length 76
	BWA-PSSM	0.807	0.967	0.795	0.998	94.35
	BWA	0.573	0.961	0.554	0.998	168.42
	BWA-MEM	0.821	0.937	0.751	0.999	65.21
	Bowtie	0.822	0.962	*	*	25.01
	Bowtie2	0.778	0.928	0.675	1.000	81.86
	GEM	0.695	0.995	*	*	32.20
d) ART single-end length 100
	BWA-PSSM	0.837	0.979	0.828	0.999	128.25
	BWA	0.308	0.973	0.302	0.998	262.54
	BWA-MEM	0.863	0.951	0.807	0.999	91.12
	Bowtie	0.855	0.976	*	*	28.33
	Bowtie2	0.811	0.944	0.668	1.000	100.49
	GEM	0.716	0.996	*	*	35.77

Comparison of sensitivity, positive predictive value (PPV) and run time using BWA-PSSM, BWA, BWA-MEM, Bowtie, Bowtie2 and GEM on simulated data sets covering a random 1% of the human genome. The reads were simulated using the ART_illumina [37] program with the default error profile for the given read length. The symbol ’*’ indicates that the mapper does not provide MapQ scores.

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ISSN: 1471-2105

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