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Table 2 Analysis of paired-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 paired-end length 36

   
 

BWA-PSSM

0.974

0.974

0.935

1.000

211.18

 

BWA

0.973

0.973

0.911

1.000

238.95

 

BWA-MEM

0.899

0.899

0.753

1.000

404.35

 

Bowtie

0.483

0.927

*

*

1578.74

 

Bowtie2

0.971

0.971

0.929

0.999

137.88

 

GEM

0.976

0.071

*

*

91.46

 b) ART paired-end length 50

   
 

BWA-PSSM

0.965

0.967

0.928

0.999

242.98

 

BWA

0.911

0.943

0.785

0.999

261.53

 

BWA-MEM

0.902

0.908

0.655

1.000

118.35

 

Bowtie

0.433

0.951

*

*

656.37

 

Bowtie2

0.939

0.952

0.736

1.000

109.78

 

GEM

0.927

0.399

*

*

48.79

 c) ART paired-end length 76

   
 

BWA-PSSM

0.958

0.978

0.943

0.999

155.57

 

BWA

0.697

0.963

0.498

0.999

210.34

 

BWA-MEM

0.939

0.943

0.815

1.000

102.00

 

Bowtie

0.366

0.969

*

*

213.10

 

Bowtie2

0.920

0.948

0.726

1.000

81.17

 

GEM

0.906

0.692

*

*

29.47

 d) ART paired-end length 100

   
 

BWA-PSSM

0.962

0.983

0.949

0.999

147.38

 

BWA

0.352

0.971

0.201

0.999

194.03

 

BWA-MEM

0.955

0.956

0.854

1.000

102.86

 

Bowtie

0.365

0.981

*

*

168.39

 

Bowtie2

0.930

0.957

0.517

1.000

74.23

 

GEM

0.900

0.779

*

*

23.25

  1. 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 insert sizes in the paired-end data were simulated using a mean length of 250 and a standard deviation of 50. The symbol ’*’ indicates that the mapper does not provide MapQ scores.
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BMC Bioinformatics

ISSN: 1471-2105

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