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.