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

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.

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