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Table 1 Assembly Results for VICUNA , SOAPdenovo and AV 454

From: De novo assembly of highly diverse viral populations

Virus

V#

Method

# output

% target region

# contigs used for

% target region

% reads

non-dominant

# genes / total

run time (s) †

memory (G) †

   

contigs

covered

reference

covered by the

align to

call rate (%)

with frame shift

  
   

(≥ 350bp)

 

guided merging

longest contig

consensus

 
 

V4526

VICUNA

10

100

1

100

95.31

0

1/11

248

0.42

  

SOAP

19

34.51

18

4.29

16.31

17.23

-a

79

6.40

  

AV 454

4

100

1

100

94.69

0

5/11

507

1.10

 

V4528

VICUNA

9

100

1

100

95.01

0

1/11

305

0.44

  

SOAP

24

39.26

22

3.75

-a

-a

-

79

6.20

WNV

 

AV 454

3

100

1

100

94.52

0

2/11

379

0.12

 

V5044

VICUNA

8

100

1

100

95.08

0

0/11

441

0.59

  

SOAP

32

40.23

28

3.16

8.84

17.45

-

117

6.40

  

AV 454

5

100

1

100

94.22

0.01

5/11

387

0.21

 

V5048

VICUNA

9

100

1

100

95.08

0

0/11

212

0.43

  

SOAP

17

24.52

15

3.49

5.67

15.90

-

90

6.40

  

AV 454

1

100

1

100

95.08

0

1/11

453

0.14

 

V4809

VICUNA

6

100

1

100

95.64

0.01

0/11

510

0.92

  

SOAP

40

59.7

33

3.63

16.05

17.78

-

184

6.50

  

AV 454

7

100

1

100

94.6

0.019

5/11

474

0.27

 

V4813

VICUNA

12

100

1

100

95.12

0.01

0/11

669

1.02

  

SOAP

49

64.33

40

3.66

18.21

18.54

-

193

6.50

DENV

 

AV 454

2

100

1

100

94.18

0.04

7/11

492

0.55

 

V4816

VICUNA

9

100

1

100

95.52

0

0/11

677

0.91

  

SOAP

37

53.85

31

3.76

11.91

16.63

-

167

6.50

  

AV 454

5

100

2

100

94.84

0.20

5/11

471

0.32

 

V4820

VICUNA

14

100

2

82.45

93.46

0

0/11

1158

1.20

  

SOAP

56

70.73

46

3.62

13.37

17.20

-

234

6.50

  

AV 454

13

100

2

76.68

91.59

0.18

6/11

462

0.17

 

V5937

VICUNA

12

100

2

93.58

93.8

0.02

0/9

516

0.86

  

SOAP

42

48.01

30

3.95

17.72

17.71

-

142

6.40

  

AV 454

16

100

1

100

86.15

0.55

6/9

406

0.15

 

V5938

VICUNA

18

100

1

100

93.69

0.01

0/9

281

0.62

  

SOAP

28

40.5

25

4.16

11.33

16.08

-

111

6.40

HIV

 

AV 454

15

100

1

100

88.01

0.43

5/9

443

0.21

 

V5943

VICUNA

9

100

1

100

95.58

0.05

1/9

96.5

0.21

  

SOAP

24

32.03

19

4.1

12.15

18.37

-

40

6.50

  

AV 454

9

97.16

1

97.16

92.52

0.80

4/9

583

0.55

 

V5945

VICUNA

13

100

2

98.83

94.44

0.09

0/9

576

0.60

  

SOAP

31

49.02

25

4.21

13.53

16.85

-

110

6.20

  

AV 454

7

100

2

83.32

89.54

1.18

4/9

465

0.17

  1. aSOAPdenovo assembly is highly fragmented, a large number of short contigs were merged using the reference genome, leading to the inclusion of many low frequency variants that considerably increased the percentage of non-dominant bases found in the assembly. In the case of sample V4528, Mosaik failed to report read alignment to the consensus. The number of genes with frame shift is not measured for SOAPdenovo. For run time and memory, †Soapdenovo uses 8 threads while the other two use 1 thread. AV 454 is run on a subset of the reads (∼ 11k, equivalent to 1% – 8% of input).
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BMC Genomics

ISSN: 1471-2164

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