Genetically improved BarraCUDA

Table 3 Mean number of paired end sequences processed per second

Prog	length	12 core server^a	GT 730^b	2 × K20	K80		Accuracy %
bwa	36 bp	1900±50	–	–	–	Mapped reads	82.05
bwa	100 bp	4500±20	–	–	–	GCAT	98.91
0.6.2	36 bp	–	3270±2 (1.7±0.05)	5300±110 (2.8±0.10)	6500±180 (3.4±0.13)	Mapped reads	83.17
0.6.2	100 bp	–	1860±4 (0.4±0.002)	8700±140 (1.9±0.03)	11700±100 (2.6±0.02)	GCAT	97.49
0.7.107	36 bp	–	7600±6 (4.0±0.11)	12900±160 (6.8±0.20)	19900±500 (10.5±0.39)	Mapped reads	83.01
0.7.107	100 bp	–	2100±14 (0.5±0.004)	8800±70 (2.0±0.02)	12800±270 (2.8±0.06)	GCAT	98.43
Improvement ratio Barracuda 0.7.107 over 0.6.2
	36 bp	–	2.32±0.003	2.43±0.06	3.07±0.11	Mapped reads	–0.16
	100 bp	–	1.13±0.01	1.00±0.02	1.09±0.02	GCAT	1.60

In (brackets) speed relative to bwa 0.7.12. ± gives standard deviation estimated from five runs. There was almost no variation in mapping rate or accuracy reported by GCAT
^a2.60GHz, see “Darwin” in Table 2
^bEstimated for two GT 730 GPUs

ISSN: 1756-0381