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Table 2 Comparison of de novo assemblies used in this study

From: A survey of the complex transcriptome from the highly polyploid sugarcane genome using full-length isoform sequencing and de novo assembly from short read sequencing

Assembly

Trinity

CLC-GWB

Velvet/OASES

SOAPdenovo-Trans

Final assembly

# contigs (> = 0 bp)

431,255

508,239

798,345

289,705

906,566

# contigs (> = 1000 bp)

210,220

109,992

37,698

34,781

294,867

# contigs (> = 2000 bp)

104,013

34,970

2,633

4,817

130,095

# contigs (> = 3000 bp)

46,942

13,732

441

1,099

57,437

# contigs (> = 4000 bp)

19,218

5,574

94

282

23,416

# contigs (> = 5000 bp)

7,542

2,413

31

104

9,227

# contigs

431,255

508,239

798,345

289,705

906,566

Largest contig

28,461

29,928

11,272

18,497

9,990

Total length

608,060,518

419,587,279

409,817,309

182,675,172

966,867,516

GC (%)

43.88

43.50

42.84

43.25

43.67

N50

2,194

1,014

516

674

1,671

N75

1,216

542

389

455

745

L50

89,618

107,715

266,636

82,953

168,723

L75

181,071

253,430

497,065

165,967

385,929

# N’s per 100 kbp

0

0

0

0

0