Table 1.
Assembly Results for VICUNA , SOAPdenovo and AV 454
|
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 |
| |
|
AV454 |
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 |
|
AV454 |
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 |
| |
|
AV454 |
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 |
| |
|
AV454 |
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 |
| |
|
AV454 |
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 |
|
AV454 |
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 |
| |
|
AV454 |
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 |
| |
|
AV454 |
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 |
| |
|
AV454 |
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 |
|
AV454 |
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 |
| |
|
AV454 |
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 |
| AV454 | 7 | 100 | 2 | 83.32 | 89.54 | 1.18 | 4/9 | 465 | 0.17 | ||
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. AV454 is run on a subset of the reads (∼ 11k, equivalent to 1% – 8% of input).