Table 2

Overview of transcriptome assembly stages

Library

ABySS a)

Inchworm a)




N50 (kb)

Max (kb) b)

Total (Mb) c)

N50 (kb)

Max (kb) b)

Total (Mb) c)




PK-Mid-flower

0.73

6.55

19.9

1.36

7.42

26.5

PK-Early-flower

0.64

4.94

16.7

1.06

6.11

24.0

PK-Pre-flower

0.80

6.74

21.4

1.56

7.89

28.0

PK-Shoot

0.69

6.16

20.2

1.34

7.41

26.8

PK-Stem

0.80

6.55

22.9

1.67

11.55

29.3

PK-Root

0.43

4.03

15.3

0.64

7.21

22.5

PK-tissue-all

0.62

8.74

26.7

-

-

-

PK-normalized1

-

-

-

1.78

10.96

31.1

PK-normalized2

-

-

-

1.72

7.89

34.2

PK-normalized3

-

-

-

1.84

8.19

34.7

PK-normalized4

-

-

-

1.71

7.10

32.1

PK-normalized-all

1.18

7.31

42.1

-

-

-



Library

Combined



N50 (kb)

Max (kb)

Total (Mb)



Non-redundant

1.65

11.55

49.4

Cap3 overlap merging

1.80

12.11

41.0


a) Fields marked with '-' indicate library/assembly combinations that were not analyzed. Statistics are shown for transcripts that passed initial QC and that could be oriented according to coding strand.

b) Size of largest transcript in the assembly

c) Total number of non-gap bases in the assembly

van Bakel et al. Genome Biology 2011 12:R102   doi:10.1186/gb-2011-12-10-r102

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