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Table 4 Evaluation of AGOUTI scaffolding in terms of gene models

From: AGOUTI: improving genome assembly and annotation using transcriptome data

  

Number of contig pairs scaffolded

Assembly

K

Total

Case 1

Case 2

Case 3

Case 4

CE1

2

3,671

3,427

92 (74)a

75 (57)

77 (67)

5

2,994

2,858

56 (40)

56 (40)

24 (21)

CE2

2

2,660

2,463

72 (55)

47 (34)

78 (68)

5

2,184

2,072

39 (29)

39 (26)

34 (27)

CE3

2

2,093

1,928

59 (44)

42 (33)

64 (60)

5

1,699

1,611

36 (24)

25 (20)

27 (25)

CE4

2

1,822

1,697

50 (39)

32 (26)

43 (38)

5

1,486

1,424

24 (16)

26 (21)

12 (10)

CE5

2

1,302

1,215

41 (34)

20 (18)

26 (21)

5

1,054

1,011

18 (13)

13 (13)

12 (8)

CE6

2

624

582

22 (19)

6 (5)

14 (10)

5

501

483

10 (7)

4 (4)

4 (1)

  1. aThe figures in parentheses show the number of consecutive contig pairs in each case