Table 2

Bowtie alignment performance versus Maq with filtered read set

Platform

CPU time

Wall clock time

Reads mapped per hour (millions)

Peak virtual memory footprint (megabytes)

Bowtie speed up

Reads aligned (%)

Bowtie

PC

16 m 39 s

17 m 47 s

29.8

1,353

-

74.9

Maq

11 h 15 m 58 s

11 h 22 m 2 s

0.78

804

38.4×

78.0

Bowtie

Server

18 m 20 s

18 m 46 s

28.3

1,352

-

74.9

Maq

18 h 49 m 7 s

18 h 50 m 16 s

0.47

804

60.2×

78.0

Performance and sensitivity of Bowtie v0.9.6 and Maq v0.6.6 when the read set is filtered using Maq's 'catfilter' command to eliminate poly-A artifacts. The filter eliminates 438,145 out of 8,839,010 reads. 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