Table 2

Comparison of assembly output with 454 reads and Illumina reads using different assemblers with different K-values.

Assembler

K-value/Seed length

N50 (bp)

Maximum contig size (bp)

Average contig size (bp)

Number of contig


454

10

8,497

28,747

3,387

290

11

7,524

28,723

3,457

284

12

8,164

26,457

3,520

279

Newbler

13

8,670

31,603

3,478

283

14

8,635

28,741

3,523

279

15

8,164

35,657

3,487

282

16

8,674

28,736

3,486

282


25

653

4,678

437

1,787

35

736

3,717

468

1,645

45

744

3,958

505

1,409

Velvet

55

731

3,515

513

1,213

65

718

2,730

556

943

75

691

3,060

574

757

85

621

3,538

584

622

95

595

3,291

600

488


MIRA

1,331

8,705

856

1,254


CLC Genomics Workbench

1,239

7,621

988

1,220


Illumina

21

4,196

23,500

1,242

954

25

5,678

40,818

1,495

809

29

6,319

35,339

1,703

705

33

4,745

32,597

1,744

659

37

4,507

22,638

1,725

637

Velvet

41

4,355

15,944

1,712

602

45

3,619

19,463

1,677

579

49

3,605

18,297

1,849

511

53

3,381

18,243

1,813

518

57

3,025

15,219

1,631

552

61

3,388

15,148

2,011

390


30

2,296

13,010

1,027

1,013

35

2,493

16,400

1,132

933

40

3,647

20,868

1,439

716

ABySS

45

4,463

20,727

1,681

578

50

5,481

22,931

2,084

453

55

5,459

23,830

2,316

401

60

6,870

22,594

2,496

386

64

4,285

16,790

1,722

524


CLC Genomics Workbench

823

8,964

454

3,572


Jiang et al. BMC Genomics 2011 12:629   doi:10.1186/1471-2164-12-629

Open Data