Table 4

Alignment evaluation on simulated & real SNPs

Simulated SNPs

Real SNPs


Program

Reads

Time (s)

Accuracy (%)

Reads

Time (s)

Accuracy (%)


Bowtie-35

24326

2

76.4

72241

4

90.5

BWA-35

24326

5

83.4

72241

8

90.2

Bowtie-76

24359

3

89.2

72241

4

93.4

BWA-76

24359

9

92.8

72241

19

92.8

Bowtie-128

24373

2

90.1

72241

5

92.4

BWA-128

24373

5

94.7

72241

49

93.4

Bowtie-512

24373

3

93.8

72241

9

93.5

BWA-512

24373

23

97.2

72241

132

91.7


Totally 94771 reads of 35, 76, 128 and 512bp were simulated from human genome build 37.1 with error rates following Sanger sequencing pattern. Such that for each read, average amount of mismatches and indels is 1 and 0.02. CPU time on a quad core of a 2.4 GHz Xeon E5620 processor with 8G RAM and accuracy in percentage are given.

Poo et al. BMC Genomics 2011 12(Suppl 3):S9   doi:10.1186/1471-2164-12-S3-S9

Open Data