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Table 2 Assembly performance comparison on the rice genome

From: Exploiting sparseness in de novo genome assembly

( k= 31 )

ABySS

Velvet

SOAPdenovo

SparseAssembler

Time (hr)

13

7

16

5

Memory peak (GB)

69

51

29

4

> 100 bp (# contigs)

458,456

397,252

444,545

386,604

   Sum (kbp)

253,708

225,618

258,106

262,988

Mean size (bp)

553

568

581

680

N50 (bp)

538

310

655

734

N95 (bp)

38

0

40

31

Corr NG50 (bp)

538

310

655

733

Corr NG95 (bp)

38

0

0

0

Longest contig (bp)

23,220

23,939

26,869

26,890

Coverage (%)

69.2

62.3

71.3

71.5

Misjoins

1

34

10

9

  1. The performance on the rice genome dataset, genome size: 370,733 kbp. Programs are run using default settings.
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BMC Bioinformatics

ISSN: 1471-2105

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