Table 1

Bowtie alignment performance versus SOAP and Maq

Platform

CPU time

Wall clock time

Reads mapped per hour (millions)

Peak virtual memory footprint (megabytes)

Bowtie speed-up

Reads aligned (%)


Bowtie -v 2

Server

15 m 7 s

15 m 41 s

33.8

1,149

-

67.4

SOAP

91 h 57 m 35 s

91 h 47 m 46 s

0.10

13,619

351×

67.3


Bowtie

PC

16 m 41 s

17 m 57 s

29.5

1,353

-

71.9

Maq

17 h 46 m 35 s

17 h 53 m 7 s

0.49

804

59.8×

74.7


Bowtie

Server

17 m 58 s

18 m 26 s

28.8

1,353

-

71.9

Maq

32 h 56 m 53 s

32 h 58 m 39 s

0.27

804

107×

74.7


The performance and sensitivity of Bowtie v0.9.6, SOAP v1.10, and Maq v0.6.6 when aligning 8.84 M reads from the 1,000 Genome project (National Center for Biotechnology Information Short Read Archive: SRR001115) trimmed to 35 base pairs. The 'soap.contig' version of the SOAP binary was used. SOAP could not be run on the PC because SOAP's memory footprint exceeds the PC's physical memory. For the SOAP comparison, Bowtie was invoked with '-v 2' to mimic SOAP's default matching policy (which allows up to two mismatches in the alignment and disregards quality values). For the Maq comparison Bowtie is run with its default policy, which mimics Maq's default policy of allowing up to two mismatches during the first 28 bases and enforcing an overall limit of 70 on the sum of the quality values at all mismatched positions. To make Bowtie's memory footprint more comparable to Maq's, Bowtie is invoked with the '-z' option in all experiments to ensure only the forward or mirror index is resident in memory at one time. CPU, central processing unit.

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

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