Table 3

Varying read length using Bowtie, Maq and SOAP

Length

Program

CPU time

Wall clock time

Peak virtual memory footprint (megabytes)

Bowtie speed-up

Reads aligned (%)

36 bp

Bowtie

6 m 15 s

6 m 21 s

1,305

-

62.2

Maq

3 h 52 m 26 s

3 h 52 m 54 s

804

36.7×

65.0

Bowtie -v 2

4 m 55 s

5 m 00 s

1,138

-

55.0

SOAP

16 h 44 m 3 s

18 h 1 m 38 s

13,619

216×

55.1

50 bp

Bowtie

7 m 11 s

7 m 20 s

1,310

-

67.5

Maq

2 h 39 m 56 s

2 h 40 m 9 s

804

21.8×

67.9

Bowtie -v 2

5 m 32 s

5 m 46 s

1,138

-

56.2

SOAP

48 h 42 m 4 s

66 h 26 m 53 s

13,619

691×

56.2

76 bp

Bowtie

18 m 58 s

19 m 6 s

1,323

-

44.5

Maq 0.7.1

4 h 45 m 7 s

4 h 45 m 17 s

1,155

14.9×

44.9

Bowtie -v 2

7 m 35 s

7 m 40 s

1,138

-

31.7

The performance of Bowtie v0.9.6, SOAP v1.10, and Maq versions v0.6.6 and v0.7.1 on the server platform when aligning 2 M untrimmed reads from the 1,000 Genome project (National Center for Biotechnology Information Short Read Archive: SRR003084 for 36 base pairs [bp], SRR003092 for 50 bp, and SRR003196 for 76 bp). For each read length, the 2 M reads were randomly sampled from the FASTQ file downloaded from the Archive such that the average per-base error rate as measured by quality values was uniform across the three sets. All reads pass through Maq's "catfilter". Maq v0.7.1 was used for the 76-bp reads because v0.6.6 does not support reads longer than 63 bp. SOAP is excluded from the 76-bp experiment because it does not support reads longer than 60 bp. 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