Table 1

Relative processing speeds of Bowtie and BWA to Oculus, for single-end and paired-end data
sa/so Bowtie 0.079 0.023
BWA 0.017 0.015

sa is the aligner’s speed, and so is Oculus's speed. Since speeds are measured in reads aligned per second, these values indicate that Oculus runs faster than the aligners, and relatively more fast for paired-end data than single-end data. As expected, Bowtie was measured to be faster than BWA, particularly for single-end data. Both aligners were run with default options.

Veeneman et al.

Veeneman et al. BMC Bioinformatics 2012 13:297   doi:10.1186/1471-2105-13-297

Open Data