Table 4.
Scaffold analysis of CABOG and Newbler assemblies
| Assembler | #Scaf. | Scaf. N50 | Scaf. max | Scaf. sum | Cov. (%) |
|---|---|---|---|---|---|
| P.gingivalis / FLX mates (M2) | |||||
| CABOG | 7 | 392 892 | 661 267 | 2 324,483 | 98.7 |
| Newbler | 9 | 268 678 | 718 704 | 2 187 430 | 94.1 |
| P.gingivalis / FLX mates+FLX mates (M1+M2) | |||||
| CABOG | 7 | 417 898 | 758 093 | 2 339 970 | 98.9 |
| Newbler | 11 | 266 698 | 718 559 | 2 183 668 | 93.9 |
| P.gingivalis / FLX reads+FLX mates (F1+M2) | |||||
| CABOG | 9 | 450 308 | 758 275 | 2 335 950 | 98.8 |
| Newbler | 382 223 | 720 519 | 2 189 593 | 94.2 | |
| P.gingivalis / FLX reads+Sanger mates (F1+S1) | |||||
| CABOG | 6 | 1 507 760 | 1 507 760 | 2 268 548 | 96.6 |
| Newbler | 51 | 1 489 797 | 1 489 797 | 2 185 214 | 94.3 |
| P.gingivalis / FLX mates+Sanger mates (M2+S1) | |||||
| CABOG | 1 | 2 317 095 | 2 317 095 | 2 317 095 | 98.7 |
| Newbler | 6 | 1 550 861 | 1 550 861 | 2 184 352 | 93.9 |
The analysis included all scaffolds 2 kb or longer found in each assembler's FASTA output. Scaffold length statistics are shown in bases excluding the lengths of the gaps between contigs. Note that scaffold sum may not equal contig sum (Table 2) due to the 2 kb threshold being applied at the scaffold not contig level. Cov, bases of the reference covered by a sum over single best alignments of each full or partial scaffold sequence.