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Table 4 Bowtie parallel alignment performance

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

  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×
  1. 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.