Table 2 Performances of assembly programs with tomato Sanger ESTs (minimum overlap: 40 bp, minimum overlap percent identity: 97%, maximum overhang: 30 bp)
From: iAssembler: a package for de novo assembly of Roche-454/Sanger transcriptome sequences
| Â | Â | 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 |
| Â | 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 | |