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Table 4 Summary of YH dataset assemblies

From: SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

Data and Program

Version

k-mer

Scaffold total length (bp)

Scaffold N50 (bp)

Contig total length (bp)

Contig N50 (bp)

Coverage

Time (h)

Peak Memory at Graph Construction (G)

SOAPdenovo YH old data

v1

25

2,837,024,602

455,380

2,327,931,678

4,933

80.51%

48^

140

SOAPdenovo YH new data

v1

31

2,901,125,426

5,806,495

2,661,982,498

12,709

81.16%

58^

107

 

v2 Multi-k-mer

45-61

2,905,148,690

22,297,138

2,799,723,051

20,926

93.91%

74^

155

 

v2 Sparse

35

2,874,598,201

18,033,622

2,767,141,367

18,856

93.17%

78^

35

 

v2 Sparse & Multi-k-mer

35-49

2,888,094,847

17,576,272

2,776,209,134

18,960

93.20%

81^

35

ALLPATHS-LG§ YH new data

42807

96

2,809,141,261

16,195,684

2,600,792,533

31,101

88.53%

249*

343

  1. To be consistence with the result of ALLPATHS-LG, contigs and scaffolds shorter than 1 kb were filtered for SOAPdenovo assemblies.
  2. § Without ‘FixLocal’ due to the module failure (see Additional file1: Supplementary Method 7).
  3. ^ Time consumption including SOAPdenovo’s error correction, assembly and gap closure modules.
  4. * Time consumption including ALLPATHS-LG’s preparation and assembly modules.