Table 5

Bowtie index building performance

Physical memory target (GB)

Actual peak memory footprint (GB)

Wall clock time

16

14.4

4 h 36 m

8

5.84

5 h 5 m

4

3.39

7 h 40 m

2

1.39

21 h 30 m

Performance results and memory footprints of running the Bowtie v0.9.6 indexer on the whole human genome (National Center for Biotechnology Information build 36.3, contigs). Runs were performed on the server platform. The indexer was run four times with different upper limits on memory usage. See Additional data file 1 (Supplementary Discussion 3 and Supplementary Table 1) for details.

Langmead et al. Genome Biology 2009 10:R25   doi:10.1186/gb-2009-10-3-r25