Table 10 Running time comparison of CUDA and OpenCL implementations of MaxSSmap (denoted by MSS)
(a) Time in minutes to map 100,000 251 bp reads to the E.coli genome. See Table 3 caption for details about reads | ||||||
|---|---|---|---|---|---|---|
Div | MSS_fast | MSS | MSS_fast | MSS | MSS_fast | MSS |
CUDA 4.2 | CUDA 6.0 | OpenCL | ||||
Reads without gaps | ||||||
.1 | 20 | 28 | 17 | 27 | 17 | 27 |
.2 | 20 | 28 | 17 | 27 | 17 | 27 |
.3 | 20 | 28 | 17 | 27 | 17 | 27 |
Reads with gaps | ||||||
.1 | 20 | 28 | 17 | 27 | 17 | 27 |
.2 | 20 | 28 | 17 | 27 | 17 | 27 |
.3 | 20 | 28 | 17 | 27 | 17 | 27 |
(b) Time in minutes to map paired human reads from NA12878 in 1000 genomes (SRR016607) of length 101 bp to the human | ||||||
genome. We denote NextGenMap by NGM and MaxSSmap by MSS. See Table 8 for more details about reads | ||||||
NGM+ | NGM+ | NGM+ | NGM+ | NGM+ | NGM+ | |
MSS_fast | MSSmap | MSS_fast | MSS | MSS_fast | MSS | |
CUDA 4.2 | s | OpenCL | ||||
1295.9 | 2242.4 | 1183.5 | 2092.7 | 1252.7 | 2159.9 | |
(c) Time in minutes to map 100,000 ancient horse DNA reads (SRR111892) of length 76 bp to | ||||||
the horse genome Equus_caballus EquCab2 (GCA_000002305.1). See Table 9 for more details | ||||||
about reads | ||||||
NGM+ | NGM+ | NGM+ | NGM+ | NGM+ | NGM+ | |
MSS_fast | MSSmap | MSS_fast | MSS | MSS_fast | MSS | |
CUDA 4.2 | CUDA 6.0 | OpenCL | ||||
1609.6 | 2836 | 1515 | 2689.8 | 1561.8 | 2736.8 | |