Table 2

Experimental results with real data

S. pneumoniae

E. coli

P. falciparum

time

% reads

bp/err

time

% reads

bp/err

time

% reads

bp/err


BWA-SW

19m

92.86

40

16m

65.4

22

8m

95.98

56

SSAHA2

6m

92.86

41

5m

65.4

23

68m

98.45

57

Newbler

11m

92.95

47

11m

65.55

24

12m

97.72

60

Segemehl

181m

90.77

61

110m

62.95

32

90m

98.14

62

GASSST

6m

89.96

63

4m

62.71

32

3m

62.80

72

TAPyR 85

2m

88.37

70

13m

59.98

35

48s

95.30

66

TAPyR 50

3m

93.33

40

20m

66.80

20

51s

98.91

53


C. elegans

D. pseudoobscura

H. sapiens

time

% reads

bp/err

time

% reads

bp/err

time

% reads

bp/err


BWA-SW

51m

61.05

19

58m

95.80

19

6s

98.25

58

SSAHA2

513m

70.40

18

92m

97.30

18

16s

99.44

54

Newbler

45m

69.07

19

119m

96.86

23

1m

98.72

78

Segemehl

249m

68.10

23

339m

90.98

28

52s

96.41

89

GASSST

9m

58.50

27

22m

82.80

30

1m

83.61

93

TAPyR 85

31m

55.59

35

7m

85.91

30

1s

95.13

96

TAPyR 50

31m

73.30

15

7m

97.05

19

2s

99.63

60


Results of the experiments performed with real biological data. These tests were run on a Linux server with 16 Gb of RAM. TAPyR was tested under two configurations, requiring alignments with at least 50% and 85% identity, designated by TAPyR 50 and TAPyR 85, respectively. The other tools were run with their default options for 454 data, except for the following modifications. SSAHA2 and Segemehl were set to report only the best alignment for each read. For GASSST, we set the minimum identity to 85% (option -p 85) to match Segemehl. Newbler was set not to generate large files (option -nobig) and to load the index into the main memory (option -m). Reported times refer to the total number of CPU-seconds that the process used directly, as given by the Linux command time -f "%U". The average base-pairs-per-error rates ("bp/err" columns) are computed based on the best reported alignment of each read only.

Fernandes et al. BMC Bioinformatics 2011 12:163   doi:10.1186/1471-2105-12-163

Open Data