Table 2. Performance comparison using different assembly pipelines.
| Sample ID |
# reads
(x10 6) |
Pipeline | # contigs | Largest contig (bp) | N50 | NG50 | Genome fraction (%) | Mis assemblies | Mismatches | Indels | Maximum RAM used (MB) |
|---|---|---|---|---|---|---|---|---|---|---|---|
| CV18 | 3.2 | VGEA SPAdes Velvet |
42 384 68 |
29928 22141 1858 |
2294 1435 728 |
29928 22141 922 |
99.776 99.652 19.326 |
0 1 0 |
10 18 3 |
0 1 0 |
627 2447 1544 |
| CV29 | 1.8 | VGEA SPAdes Velvet |
31 478 66 |
7731 24904 2877 |
3065 1136 942 |
7534 24904 1380 |
99.786 99.632 1.729 |
0 0 0 |
9 7 0 |
0 0 0 |
484 2314 807 |
| CV45 | 6.2 | VGEA SPAdes Velvet |
30 45 535 |
16248 6779 5239 |
2603 1255 898 |
16248 2447 3030 |
98.291 94.957 14.256 |
1 0 0 |
11 35 0 |
0 12 0 |
666 2504 1360 |
| CV115 | 2 | VGEA aSPAdes Velvet |
28 49 41 |
5225 1942 2847 |
2258 1068 819 |
3060 1828 931 |
96.957 - 68.134 |
0 – 0 |
12 – 9 |
0 – 0 |
177 1735 511 |
| CV145 | 4.4 | VGEA SPAdes Velvet |
28 188 178 |
6807 3216 1798 |
2049 1190 682 |
4214 2477 1107 |
73.093 5.073 3.578 |
0 2 0 |
14 13 0 |
0 0 0 |
635 2547 1459 |
Notes.
a
QUAST gave no genome fraction value for this sample.