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Table 3 ContigExtender results on NIBSC datasets using MetaSPAdes assembly outputs as seed contigs

From: ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data

Contig ID

Meta SPAdes (bp)

Contig Extender (bp)

Gained length (bp)

Gained (%)

Aligned (bp)

Aligned (%)

Viral genome (Accession)

Genome size (bp)

Gained genome (%)

PRICE (bp)

GenSeed (bp)

Kollector (bp)

Depth (x)

1

4251

10,059

5808

137

10,057

100

Human_rubulavirus_2 (NC_003443.1)

15,646

37

   

54

2

3114

8315

5201

167

8288

100

Human_mastadenovirus_C (NC_001405.1)

35,937

14

   

31

3

4705

6841

2136

45

6814

100

Human_mastadenovirus_C (NC_001405.1)

35,937

6

   

36

4

4118

5099

981

24

5057

99

Human_mastadenovirus_C (NC_001405.1)

35,937

3

   

36

5

2818

5063

2245

80

5062

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

2

   

14

6

2234

4671

2437

109

4675

100

Human_betaherpesvirus_5 (NC_006273.2)

235,646

1

   

28

7

1784

4224

2440

137

4224

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

2

   

11

8

3944

4171

227

6

4149

99

Human_mastadenovirus_C (NC_001405.1)

35,937

1

   

29

9

3051

4098

1047

34

4092

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

1

   

16

10

3158

4029

871

28

3575

89

Human_betaherpesvirus_5 (NC_006273.2)

235,646

0

   

42

11

3462

3964

502

15

3961

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

0

   

23

12

1789

3666

1877

105

3665

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

2

   

14

13

1761

3379

1618

92

3319

98

Rotavirus_A (NC_011507.2)

3302

49

3403

  

126

14

1759

3292

1533

87

2552

78

Bat_rotavirus (NC_040413.1)

2649

58

2274

 

2101

267

15

2748

3140

392

14

3146

100

Human_betaherpesvirus_5 (NC_006273.2)

235,646

0

   

24

16

2861

3115

254

9

3115

100

Human_respirovirus_1 (NC_003461.1)

15,600

2

   

29

17

2664

3016

352

13

3016

100

Human_mastadenovirus_C (NC_001405.1)

35,937

1

   

25

18

1525

2839

1314

86

2840

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

1

   

7

19

1958

2616

658

34

2612

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

1

   

27

20

1789

2213

424

24

2213

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

0

   

8

21

1889

2154

265

14

2154

100

Human_betaherpesvirus_5 (NC_006273.2)

235,646

0

   

29

22

1881

2093

212

11

2093

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

0

   

19

23

1748

2001

253

14

1996

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

0

   

14

24

1699

1931

232

14

1931

100

Human_alphaherpesvirus_3 (NC_001348.1)

124,884

0

   

21

25

1505

1846

341

23

1847

100

Human_betaherpesvirus_5 (NC_006273.2)

235,646

0

   

27

26

1508

1768

260

17

1770

100

Human_betaherpesvirus_5 (NC_006273.2)

235,646

0

   

26

  1. Columns 2–14 are: 2) seed contig length generated by MetaSPAdes; 3) extended contig length from seed contig; 4) gained length from ContigExtender (column 3 subtracted by column 2); 5) gained length as percentage of seed contig (column 4 divided by column 2); 6) the largest contiguous segment length of extended contig that are aligned to reference genome; 7) percentage of the alignment segment of the extend contig; 8) reference viral genome; 9) viral genome size; 10) gained length from ContigExtender as percentage of viral genome (column 4 divided by column 9); 11) gained extension by PRICE; 12) gained extension by GenSeed; 13) gained extension by Kollector; 14) average sequencing depth of the extended contig. Entries in the PRICE, GenSeed, and Kollector columns are blank if they produced no extension
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BMC Bioinformatics

ISSN: 1471-2105

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