Table 1.
Results and characteristics of assemblies run with different parameter settings.
| Gap Penalty | |||||
|---|---|---|---|---|---|
| 30 | 50 | ||||
| Match % | Match length | Number of contigs and average length | Number of assembled reads | Number of contigs and average length | Number of assembled reads |
| 85% | 19 | 50,689 (537) | 255,711 | 51,058 (533) | 252,299 |
| 23 | 49,621 (516) | 248,537 | 50,039 (513) | 245,563 | |
| 25 | 48,962 (507) | 244,120 | 49,366 (504) | 241,289 | |
| 90% | 19 | 55,886 (499) | 220,517 | 55,996 (497) | 217,169 |
| 23 | 53,724 (490) | 213,344 | 53,824 (488) | 209,916 | |
| 25 | 52,770 (485) | 209,735 | 52,726 (483) | 206,167 | |
| 95% | 19 | 51,289 (443) | 156,578 | 51,908 (441) | 154,605 |
| 23 | 46,611 (441) | 142,428 | 46,585 (439) | 140,071 | |
| 25 | 44,752 (439) | 137,096 | 44,674 (437) | 134,566 | |
| Combination of reference-based (match % = 88) and de novo assemblies (match % = 93) | |||||
| 88%,93% | 19 | 63,687 (500) | 225,517 | ||
Results from assemblies run in Seqman Ngen with different starting values for gap penalty, minimum match size, and mimimum match percentage. We present the number of contigs, average contig size (in parentheses), and the number of reads assembled into contigs for each different set of parameter settings.