Table 2. Comparison of different filtering strategies for D. melanogaster.

Method	Data		Assembly size (Mb)	Assembled genome (Mb)	Accuracy	Recall	N50	Reads (million)
Untrimmed	SRR063698	full	120.5	106.0	0.88	0.63	6,939	54.3
		reduced	113.4	84.4	0.74	0.50	1,717	13.7
	SRR063699	full	108.1	77.4	0.72	0.45	1,278	26.8
		reduced	63.6	41.2	0.65	0.24	411	6.7
ConDeTri	SRR063698	full	118.9	102,8	0.86	0.61	8,222	43.4
		reduced	103.6	65.9	0.64	0.39	1,007	11.0
	SRR063699	full	77.5	59.0	0.76	0.35	508	10.0
		reduced	23.4	18.0	0.77	0.11	234	2.5
SolexaQA	SRR063698	full	115.7	93.7	0.81	0.56	5,691	37.8
		reduced	93.4	51.5	0.55	0.31	677	9.6
	SRR063699	full	60.5	40.2	0.66	0.24	408	8.7
		reduced	16.7	11.6	0.70	0.07	203	2.2
Quake	SRR063698	full	114.3	81.6	0.71	0.48	21,615	49.6
		reduced	70.6	16.5	0.23	0.10	683	10.4
	SRR063699	full	1.9	0.1	0.06	0.00	6,678	5.9
		reduced	1.4	0.1	0.04	0.00	3,808	1.3
Bwa	SRR063698	full	119.4	99.1	0.83	0.59	13,953	46.2
		reduced	107.0	70.1	0.66	0.42	1,264	11.7
	SRR063699	full	92.2	58.1	0.63	0.34	732	17.4
		reduced	47.5	33.0	0.70	0.20	294	4.4

Assembly size, size of assembled D. melanogaster reference genome, recall, accuracy, N50 size and number of reads using the different data sets.