Table 4

Bowtie parallel alignment performance

CPU time

Wall clock time

Reads mapped per hour (millions)

Peak virtual memory footprint (megabytes)

Speedup

Bowtie, one thread

18 m 19 s

18 m 46 s

28.3

1,353

-

Bowtie, two threads

20 m 34 s

10 m 35 s

50.1

1,363

1.77×

Bowtie, four threads

23 m 9 s

6 m 1 s

88.1

1,384

3.12×

Performance results for running Bowtie v0.9.6 on the four-core server with one, two, and four threads. Other experimental parameters are identical to those of the experiments in Table 1. CPU, central processing unit.

Langmead et al. Genome Biology 2009 10:R25   doi:10.1186/gb-2009-10-3-r25