Table 1. Comparison of assembly software: number and size of contigs, errors and time/memory requirements.
| Assembly | PBcR | Canu | Miniasm | Miniasm & Nanopolish | SPAdes | Illumina | Manually finished |
|---|---|---|---|---|---|---|---|
| Number of contigs | 21 | 15 | 16 | 16 | 13 | 90 | 10 |
| Number of bases | 5490929 | 5542520 | 5843777 | 5673354 | 5576147 | 5454767 | 5586413 |
| Largest contig (bases) | 1615977 | 2782732 | 1548218 | 1504104 | 5303011 | 686305 | 5031167 |
| Mean contig (bases) | 261473 | 369501 | 365236 | 354585 | 428934 | 60608 | 620713 |
| N50* | 1197808 | 2782732 | 661959 | 641515 | 5303011 | 153115 | 5031167 |
| Total mis-assemblies | 5 | 2 |
0 (analysis failed) |
3 | 5 | 6 | na |
| Mismatches per kb | 1.0038 | 0.3494 | 6.6578 | 5.4843 | 0.0371 | 0.0355 | na |
| Indels per kb | 12.1668 | 7.769 | 18.6418 | 8.987 | 0.0353 | 0.0322 | na |
| Memory requirement | 7 GB | 8 GB | 3 GB | 3 GB & 4 GB | 2 GB | 4 GB | na |
| Run time | 8 h | 2 h | 2 min |
2 min & 3 days 11 h |
3 h | 3 h | na |
| Total CPU time† | 79728 | 54745 | 124 | 9450274 | 9164 | 12514 | na |
| Number of threads | 16 | 8 | 2 | 2 & 16 | 16 | 2 | na |
*N50: a weighted median statistic. Half (50 %) of the assembly is contained in contigs greater than or equal to a contig of this size.
†Total CPU (Central Processing Unit) time: The amount of time used by the CPUs actively processing instructions. Run time, or ‘real’ time, may be longer, as it includes idle time or time spent waiting for input or output, or may be shorter if the workload is shared between more than one CPU.