Table 2 Performance comparison using different assembly pipelines
Virus1 | # reads (x 106) | Pipeline | # contigs | Largest contig (bp) | N50 | NG50 | # fully un-aligned contigs | REAPR score | Run time (h) | # thread (4GB/CPU) |
|---|---|---|---|---|---|---|---|---|---|---|
HSV-1 laboratory strain | 33 | VirAmp | 5 | 108,094 | 108,094 | 108,094 | 0 | 1.28e + 10 | 1.5 | 1 |
SPAdes | 9,609 | 107,857 | 258 | 107,857 | 9582 | 4.12e + 7 | 6 | 4 | ||
VICUNA | 266 | 19,285 | 5,654 | 8,704 | 163 | 6.01e + 8 | 8 | 6 | ||
HSV-1 w/ fluorescent insert | 37 | VirAmp | 4 | 63,109 | 49,971 | 49,971 | 0 | 4.00e + 9 | 2.5 | 1 |
SPAdes | 5,946 | 39,441 | 273 | 13,888 | 5898 | 4.48e + 7 | 7 | 4 | ||
VICUNA | 101 | 33,391 | 9,822 | 7,644 | 60 | 9.03e + 8 | 13 | 6 | ||
HSV-1 clinical isolate | 87 | VirAmp | 3 | 117,134 | 117,134 | 117,134 | 0 | 1.24e + 9 | 4 | 1 |
SPAdes | 74,927 | 93,771 | 256 | 82,041 | 74,608 | 2.97e + 8 | 21 | 4 | ||
VICUNA | 424 | 23,611 | 2,786 | 7,136 | 383 | 2.19e + 8 | 30 | 6 |