Table 2.

Performances of assembly programs with tomato Sanger ESTs (minimum overlap: 40 bp, minimum overlap percent identity: 97%, maximum overhang: 30 bp)

		iAssembler	CAP3	MIRA	TGICL	Phrap	Newbler
No. unigenes		53,734	89,590	84,993	51,502	43,434	49,792
Average unigene length (bp)		920.6	735.2	741.4	920.1	963.7	997.7
No. type I errors	identity < 97%	5	85	26,224	2,602	11,223	8,059
	overhang > 30 bp	3	156	8,282	5,743	34,148	21,540
No. type II errors		254	14,396	12,075	3,036	3,909	5,868
Total assembly errors		262	14,637	46,581	11,381	49,280	35,467
Run Time (minute)		634	369	230	450	175	42