Table 2.

Accuracy assessment of MapReduce-Inchworm compared to the original Inchworm using three simulated read datasets for mouse RNA-Seq

				Number of pair-end reads
				100 M	150 M	200 M
REF-EVAL	Contig	Recall	Original	0.3098	0.3122	0.3126
			MapReduce	0.3274	0.3308	0.3314
		Precision	Original	0.3258	0.3283	0.3280
			MapReduce	0.3389	0.3419	0.3422
	Nucleotide	Recall	Original	0.9752	0.9764	0.9779
			MapReduce	0.9763	0.9783	0.9793
		Precision	Original	0.9847	0.9845	0.9845
			MapReduce	0.9870	0.9869	0.9869
		N1	Original	32,712	39,273	43,862
			MapReduce	33,687	40,452	45,344
		N2	Original	16	20	26
			MapReduce	4	12	8

Statistics from the REF-EVAL component of DENONATE [41], for three simulated read datasets. Recall is the fraction of reference elements that are correctly recovered by an assembly. Precision is the fraction of assembly elements that correctly recover a reference element. At the Contig level, a 99% alignment cutoff has been used to identify a recovered transcript (left-hand bars in Fig. 3). Original refers to the results of Trinity run with the original version of Inchworm. MapReduce refers to the results of Trinity run with the MapReduce-Inchworm method presented here. Also shown are the N1 and N2 statistics, as given by the script FL_trans_analysis_pipeline.pl. N1 represents the total number of assembled transcripts that give full-length matches to the reference. N2 represents the number of fused transcripts. For comparison, there are 80,867 reference transcripts