Table 2 Summary of assembly statistics generated by various pipelines.

From: De novo transcriptome assembly and analysis of the freshwater araphid diatom Fragilaria radians, Lake Baikal

Workflow*

Velvet/Oases

Trinity

1

2

1

2

General assembly metrics

Lenght, Mbp

11.37

17.92

16.64

41.76

Number of transcripts

9,076

22,275

13,285

28,263

N50, bp

1,726

945

1,695

1,944

L50

2,099

6,446

3,112

6,840

Transrate

Score

0.13

0.10

0.18

0.39

Optimal score

0.16

0.12

0.22

0.44

Optimal cutoff

0.26

0.24

0.29

0.35

Good contigs, %

79

80

80

87

BUSCO results**

Complete

120

62

167

267

Fragmented

18

95

18

7

Missed

165

146

118

29

  1. *(1) assemble samples → merge assemblies (AM); (2) merge reads → assemble (MA).
  2. **BUSCO Eukarya database OrthoDB v.9, 303 busco genes.
Back to article page