Table 5

Comparison of the runtime and memory usage on the human chromosome 14 assembly.

Evaluations

Wall-clock time (Hr.)

Speedup against 1 thread

Peak memory usage (GB)

Thread # in total

Machine #

K-mer size #

Tile #


Velvet 61k

0.95

1x

8.26

1

1

1

1


Velvet 61k

0.47

2.02x

8.40

4

1

1

1


SOAPdenovo 55k

0.43

1x

8.31

1

1

1

1


SOAPdenovo 55k

0.25

1.72x

8.50

4

1

1

1


Tiger-Velvet-I 1i

4.69

1x

1.87

1

1

1

150


Tiger-Velvet-I 1i

1.58

2.98x

2.44

4

1

1

150


Tiger-Velvet-I 1i

0.83

5.69x

N/A+

12

3

1

150


Tiger-Velvet-I 1i

0.66

7.16x

N/A+

20

5

1

150


"#k" stands for the applied k-mer size. "#i" stands for the iteration number.

+ The memory usage across machines can not be measured in our environment.

Wu et al. BMC Bioinformatics 2012 13(Suppl 19):S18   doi:10.1186/1471-2105-13-S19-S18

Open Data