BASE: a practical de novo assembler for large genomes using long NGS reads

BMC Genomics

Table 5 Acceleration performance of GPU on BWT construction

	Read_num	Read_length	With GPU	Without GPU	Time fold
S.aureus MW2	6,720,000	100	133 s	184 s	1.38
V.para	4,896,000	250	329 s	514 s	1.56
YH, 100 bp	1,057,750,382	100	5 h	19 h	3.80
NA12878, 150 bp	770,960,980	150	7 h	30 h	4.29

To evaluate the acceleration performance of GPU on BWT construction, we used two versions, one of which used GPU and the other not, to build bi-directional BWT on four datasets. The results showed that especially in large genome dataset, compared with GPU version, version without GPU costs ~4 fold more time to construct BWT

ISSN: 1471-2164