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Table 2 Transcriptome assembly statistics

From: Optimizing and benchmarking de novo transcriptome sequencing: from library preparation to assembly evaluation

Assembly No.

Individuala or integratedb assembly

Assembly approach

Number of fragments (×106) c

Raw assembly

Assembly filtered by mapping count (≥5)

N50 length (bp)

Number of contigs

Number of subcomponents

Number of contigs

Number of subcomponents

1

A

Trinity

22.719

222178

168924

106323

62636

3091

2

B

21.224

228165

159338

94371

45267

3634

3

C

3.569

104985

83417

37504

22331

3093

4

D

23.712

417291

291424

204328

104294

3693

5

E

16.037

383737

246347

149926

56669

4149

6

F

75.929

798982

562528

358433

182611

3956

7

G

82.453

787608

541906

375297

191055

3860

8

H

81.033

525154

348570

250433

115476

4090

9

Integrated

All-in-one by Trinity

326.676

1214573

852257

653132

387456

2680

10

All-in-one by SOAPdenovo-trans, multiple k-mer lengths

326.676

1087900

745363

748019

422329

4854

11

Assembly following Trinity’s normalization

39.593d

1465425

721986

972512

330937

3755

12

Assembly after khmer

33.251d

1464412

741241

945799

314023

2898

13

Assembly and clustering

326.676

1562282

939252

996336

457323

3897

  1. aCorresponding library symbols (see Table 1) are included for individual assemblies
  2. bIntegration of all the individual assemblies
  3. cNumber of fragments for which both of the pairs passed quality control
  4. dNote that this is a number of fragments after in silico normalization