SeQual-Stream: approaching stream processing to quality control of NGS datasets

BMC Bioinformatics

Table 6 Runtimes (in seconds) and corresponding speedups of SeQual-Stream over SeQual for the SRR114 dataset and different quality control operations (“Downloading” scenario, testbed 1)

Operation	Dataset	Mode	Nodes	SeQual	SeQual-Stream	Speedup
QUALITY	SRR114	Single	1	2599	1373	1.89
			2	1929	1134	1.70
			4	1602	1024	1.56
			8	1225	864	1.42
			16	1083	858	1.26
		Paired	1	7703	3490	2.21
			2	6087	2869	2.12
			4	3846	1920	2.00
			8	2805	1548	1.81
			16	2172	1518	1.43
NONIUPAC	SRR114	Single	1	2500	1818	1.37
			2	1960	1273	1.54
			4	1407	918	1.53
			8	1175	843	1.39
			16	1090	829	1.31
		Paired	1	7578	3611	2.10
			2	6764	2959	2.29
			4	3818	1891	2.02
			8	2366	1561	1.52
			16	2159	1559	1.38
TRIMRIGHTP	SRR114	Single	1	3215	1529	2.10
			2	1741	1174	1.48
			4	1410	1019	1.38
			8	1209	838	1.44
			16	1089	829	1.31
		Paired	1	6680	3363	1.99
			2	5874	2659	2.21
			4	4049	1828	2.21
			8	2579	1522	1.69
			16	2140	1501	1.43
DNATORNA	SRR114	Single	1	3509	1953	1.80
			2	2372	1678	1.41
			4	1506	1079	1.40
			8	1219	863	1.41
			16	1082	813	1.33
		Paired	1	7042	4290	1.64
			2	6267	2668	2.35
			4	4370	1780	2.45
			8	3008	1559	1.93
			16	2176	1488	1.46

ISSN: 1471-2105