Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

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.

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