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).

Yang et al.

Yang et al. BMC Genomics 2012 13:475   doi:10.1186/1471-2164-13-475

Open Data