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Table 1 Comparison of runtime between the JA algorithm and our algorithm on an input with 8 million reads from a plant genome

From: Efficient parallel and out of core algorithms for constructing large bi-directed de Bruijn graphs

  

JA ALGO

ParBiConstruct

P

k

U(sec)

S(sec)

R(mm:ss)

U(sec)

speedup

S(sec)

speedup

R(mm:ss)

Speedup

8

21

6388.08

21.54

13:26.42

1028.61

6.21

8.08

2.67

2:10.77

6.17

8

27

2220.41

14.85

5:47.71

500.22

4.44

3.72

3.99

1:04.12

5.42

8

33

1662.14

6.63

3:29.89

288.14

5.77

2.47

2.68

0:37.46

5.60

8

35

496.89

3.81

1:03.77

159.59

3.11

1.03

3.70

0:21.19

3.01

12

21

9116.72

20.31

12:43.14

985.97

9.25

6.91

2.94

1:23.95

9.09

12

27

2626.30

13.94

3:59.85

479.10

5.48

3.20

4.36

0:41.32

5.80

12

33

2320.07

6.14

3:15.15

317.08

7.32

2.35

2.61

0:27.76

7.03

12

35

561.02

3.47

0:48.19

166.06

3.38

1.13

3.07

0:15.04

3.20

16

21

11943.18

19.91

12:29.49

1044.31

11.44

7.42

2.68

1:06.91

11.20

16

27

2889.32

12.95

3:50.81

498.36

5.80

3.42

3.79

0:32.48

7.11

16

33

2971.37

6.49

3:07.41

357.63

8.31

2.53

2.57

0:23.64

7.93

16

35

580.08

3.67

0:37.63

170.56

3.40

1.33

2.76

0:11.85

3.18

24

21

17744.55

20.26

12:21.94

1205.51

14.72

8.00

2.53

0:51.74

14.34

24

27

3399.06

15.24

2:39.02

658.02

5.17

4.00

3.81

0:28.72

5.54

24

33

4981.96

7.89

6:25.41

652.80

7.63

3.69

2.14

0:51.65

7.46

24

35

750.26

5.57

0:37.30

295.58

2.54

2.23

2.50

0:14.19

2.63

32

21

23119.80

20.95

12:04.89

1070.31

21.60

8.40

2.49

0:34.90

20.77

32

27

3897.63

15.20

2:12.96

464.24

8.40

5.21

2.92

0:15.81

8.41

32

33

5132.44

9.33

3:11.64

534.38

9.60

4.84

1.93

0:21.01

9.12

32

35

973.78

5.35

0:37.30

324.23

3.00

3.35

1.60

0:13.16

2.83

48

21

37116.65

26.37

13:03.67

2422.83

15.32

13.46

1.96

0:55.33

14.16

48

27

4932.47

21.70

1:48.76

1112.72

4.43

10.51

2.06

0:26.11

4.17

48

33

6658.10

13.72

3:11.84

1157.33

5.75

9.41

1.46

0:34.33

5.59

48

35

1020.88

10.95

0:30.47

447.84

2.28

8.18

1.34

0:14.08

2.16

64

21

51443.09

35.46

16:25.33

1938.25

26.54

25.05

1.42

0:39.57

24.90

64

27

6304.66

33.49

2:05.96

1029.89

6.12

21.80

1.54

0:21.64

5.82

64

33

15314.25

23.95

5:57.82

673.55

22.74

21.31

1.12

0:17.08

20.95

64

35

1048.56

20.71

0:25.93

358.62

2.92

18.86

1.10

0:09.87

2.63

  1. Input Reads: 8388608 short reads, each of size 36 base pairs
  2. Average User time speed up = 8.310X
  3. Average System time speed up = 2.490X
  4. Average Real time speed up = 8.079X