Table 4.
Basic assembly metrics
| CAP3 | CLC | MIRA | Newbler 2.3 | Newbler 2.5 | SeqMan | |
|---|---|---|---|---|---|---|
| Number of contigs† | 24727 | 22746 | 35827 | 12019 | 21734 | 29969 |
| Total Bases | 16733217 | 14875522 | 21339704 | 14456476 | 20066883 | 21355682 |
| Number of contigs (> = 1 kbp) | 4403 | 4174 | 4770 | 6320 | 7661 | 6082 |
| Total Bases (in contigs > = 1 kbp) | 6461079 | 6255785 | 7027775 | 10810962 | 13691429 | 9296011 |
| Max contig length | 4011 | 4368 | 5784 | 5872 | 6228 | 6263 |
| Mean contig length | 677 | 654 | 596 | 1203 | 923 | 713 |
| N50 | 806 | 850 | 708 | 1487 | 1448 | 880 |
| Number of contigs in N50 | 6533 | 5459 | 9148 | 3406 | 4649 | 7555 |
| Reads used (SSAHA2) | 670425 | 679152 | 672036 | 616672 | 667597 | 681974 |
| Multi-hit reads (SSAHA2) | 271648 | 118334 | 392884 | 249210 | 352887 | 322409 |
| Reads used (CLC) | 690889 | 691818 | 696527 | 600132 | 681831 | 711726 |
| Multi-hit reads (CLC) | 91951 | 24485 | 162365 | 213670 | 262178 | 128631 |
| Time taken | 1 day* | 4 minutes * | 3 days * | 2 hours * | 45 minutes * | 6 hours ** |
† only contigs > 100 bases were assessed
* on a dual quad-core 3 GHz Xeon workstation with 32 GB RAM
** on a dual core 2.53 GHz Mac mini server with 4 GB RAM