Adaptable probabilistic mapping of short reads using position specific scoring matrices

BMC Bioinformatics

Table 5 Analysis of the xeno mapping experiment

		MapQ filtered
	Mapper	Sensitivity	PPV	Time (s)
a) Xeno short reads (SRR001981)
	BWA-PSSM^EVO	0.305	0.982	3721.53
	BWA-PSSM	0.269	0.976	3228.94
	BWA	0.268	0.982	1444.48
	BWA-MEM	0.186	0.989	727.22
	Bowtie2	0.195	0.981	635.21
b) Xeno long low quality reads (SRR023647)
	BWA-PSSM^EVO	0.609	0.994	9355.64
	BWA-PSSM	0.591	0.989	7371.12
	BWA	0.550	0.992	3420.15
	BWA-MEM	0.500	0.984	1260.17
	Bowtie2	0.429	0.991	1262.93
c) Xeno long high quality reads (SRR516029)
	BWA-PSSM^EVO	0.364	0.979	13271.88
	BWA-PSSM	0.300	0.972	11457.96
	BWA	0.302	0.984	5735.58
	BWA-MEM	0.429	0.988	4147.98
	Bowtie2	0.218	0.987	3468.82

Comparison of sensitivity, positive predictive value (PPV) and run time using BWA-PSSM, BWA, BWA-MEM and Bowtie2 on real single-end reads from D. melanogaster mapped to D. simulans. In BWA-PSSM^EVO we include an evolutionary model reflecting the substitution rate between the two Drosophila genomes when mapping the reads to D. simulans, while in the BWA-PSSM results we only include the standard error model. The reported running time is only for the xeno mapping.

ISSN: 1471-2105