Table 7 Runtimes (in seconds) and corresponding speedups of SeQual-Stream over SeQual for the SRR589 paired-end dataset (“Downloaded” scenario, testbed 2)
From: SeQual-Stream: approaching stream processing to quality control of NGS datasets
Operation | Dataset | Mode | Nodes | SeQual | SeQual-Stream | Speedup |
|---|---|---|---|---|---|---|
QUALITY | SRR589 | Paired | 1 | 9369 | 5137 | 1.82 |
2 | 7666 | 4629 | 1.66 | |||
4 | 5152 | 3059 | 1.68 | |||
8 | 3418 | 2728 | 1.25 | |||
NONIUPAC | SRR589 | Paired | 1 | 13253 | 5558 | 2.38 |
2 | 7703 | 4498 | 1.71 | |||
4 | 4887 | 3307 | 1.48 | |||
8 | 3172 | 2818 | 1.13 | |||
TRIMRIGHTP | SRR589 | Paired | 1 | 13343 | 5875 | 2.27 |
2 | 7532 | 4172 | 1.81 | |||
4 | 4813 | 3018 | 1.59 | |||
8 | 3085 | 2718 | 1.14 | |||
DNATORNA | SRR589 | Paired | 1 | 10256 | 5668 | 1.81 |
2 | 7346 | 5468 | 1.34 | |||
4 | 5179 | 3098 | 1.67 | |||
8 | 3196 | 2758 | 1.16 |