Table 2.
CABOG and Newbler assemblies of hybrid data sets
| Assembler | #Contigs | Contig N50 | Contig Max | Contig Sum |
|---|---|---|---|---|
| P.gingivalis / FLX reads+FLX mates (F1+M2) | ||||
| CABOG | 48 | 67 993 | 205 585 | 2 332 097 |
| Newbler | 119 | 27 561 | 134 859 | 2 183 278 |
| P.gingivalis / FLX reads+Sanger mates (F1+S1) | ||||
| CABOG | 65 | 51 745 | 169 923 | 2 266 305 |
| Newbler | 104 | 32 377 | 154 008 | 2 184 009 |
| P.gingivalis / FLX mates+Sanger mates (M2+S1) | ||||
| CABOG | 34 | 101 101 | 307 732 | 2 314 836 |
| Newbler | 115 | 29 216 | 110 686 | 2 179 717 |
| E.coli / FLX reads+FLX mates (F2+M1) | ||||
| CABOG | 22 | 440 632 | 861 331 | 4 642 198 |
| Newbler | 87 | 87 223 | 240 232 | 4 516 116 |
| P.sp CNPT3 / FLX reads+Sanger mates (F1+S1) | ||||
| CABOG | 39 | 126 165 | 336 216 | 2 992 650 |
| Newbler | 70 | 79 879 | 203 365 | 2 963 428 |
| P.sp CNPT3 / FLX reads+Sanger mates (F2+S1) | ||||
| CABOG | 42 | 138 508 | 365 104 | 2 983 118 |
| Newbler | 99 | 45 693 | 171 391 | 2 951 683 |
| C.muris / FLX reads+Sanger mates (F1+S1) | ||||
| CABOG | 69 | 323 162 | 819 035 | 9 186 849 |
| Newbler | 73 | 247 897 | 731 211 | 9 097 078 |
The analysis included all contigs 2 kb or longer found in each assembler's FASTA output. N50, the length of the shortest contig required to span 50% of the genome length; Max, the length of the longest contig, Sum, the total contig span. Contig size statistics are shown in bases. The codes in parentheses refer to component datasets described in Table 1. Assemblies are compared by contig size statistics. Selected combinations are shown; others are provided in the Supplementary Material.