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Table 1 Relative processing speeds of Bowtie and BWA to Oculus, for single-end and paired-end data

From: Oculus: faster sequence alignment by streaming read compression

  

SE

PE

sa/so

Bowtie

0.079

0.023

 

BWA

0.017

0.015

  1. 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.
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BMC Bioinformatics

ISSN: 1471-2105

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