Removing Noise From Pyrosequenced Amplicons

BMC Bioinformatics

Table 5 Run times in seconds for AmpliconNoise and the original PyroNoise for the V5 'Artificial Community' data set

	AmpliconNoise			PyroNoise
Process	Cores	Wall	CPU	Cores	Wall	CPU
Initial pairwise distances (NDist)	64	1900	45358	64	1900	45358
Initial clustering (FCluster)	1	292	252	1	292	252
Flowgram clustering (PyroNoise)	64	1904	9364	64	55241	686497
Sequence clustering (SeqNoise)	64	503	20713	--	--	--
Total		4599	75687		57433	732107

The results are for a Xeon Linux cluster running programs across a maximum of 64 cores. Two times in seconds are quoted for each step, wall (time) is the true time elapsed between the start and end of a process and CPU (time) is the total time over all cores spent on actual calculations.

ISSN: 1471-2105