Skip to main content

Table 3 Performances of assembly programs with olive Roche-454 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

  

iAssembler

CAP3

MIRA

TGICL

Phrap

Newbler

No. unigenes

77,572

10,5103

127,565

80,540

70,489

69,301

Average unigene length (bp)

231.5

214.5

209.7

221

246.5

227.4

No. type I errors

identity < 97%

1

569

3

3,668

18,071

8,317

 

overhang > 30 bp

1

11

2

1,621

5,066

11,266

No. type II errors

35

12,279

14,821

4,420

4,752

1,518

Total assembly errors

37

12,859

14,826

9,709

27,889

21,101

Run Time (minute)

227

79

57

101

43

7