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Table 2 Bowtie alignment performance versus Maq with filtered read set

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

  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
  1. 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.