Table 3 |
|||||||
| Genome assembly continuity and correctness comparison to secondary technologies | |||||||
| Organism | Assembled with | Assembly bp | Contigs | N50 | LAP | Discordant bases | QV |
| E. coli K12 | MiSeq 100× 2×150 bp 300 bp (MaSuRCA iCORN) | 4,682,345 | 139 | 113,852 | -9.68E + 07 | 28 | 52.23 |
| 454 50× | 4,569,757 | 93 | 117,490 | -9.73E + 07 | 17 | 54.29 | |
| PBcR 200× | 4,653,486 | 1 | 4,653,486 | -9.64E + 07 | 3 | >60 | |
| E .coli O157:H7 | MiSeq 100× 2×150 bp 500 bp (SPAdes iCORN) | 5,433,737 | 413 | 133,641 | -3.67E + 07 | 62 | 49.43 |
| 454 22× + 8× 5 kbp + 10× 10 kbp | 5,347,050 | 409 | 133,665 | -3.73E + 07 | 66 | 49.09 | |
| PBcR 200× | 5,611,389 | 9 | 4,324,437 | -3.66E + 07 | 0 | >60 | |
| B. trehalosi | MiSeq 100× 2×150 bp 500 bp (SPAdes iCORN) | 2,377,594 | 83 | 222,446 | -3.31E + 07 | 10 | 53.76 |
| 454 50× | 2,364,704 | 66 | 117,742 | -3.32E + 07 | 9 | 54.20 | |
| PBcR 200× | 2,411,068 | 1 | 2,411,068 | -3.27E + 07 | 0 | >60 | |
| M. haemolytica | MiSeq 100× 2×150 bp 500 bp (MaSuRCA iCORN) | 2,721,965 | 89 | 84,094 | -3.33E + 07 | 47 | 47.63 |
| PBcR 200× | 2,736,037 | 1 | 2,736,037 | -3.31E + 07 | 0 | >60 | |
| F. tularensis | MiSeq 100× 2×250 bp 500 bp (SPAdes iCORN) | 1,825,374 | 130 | 24,065 | -1.33E + 07 | 0 | >60 |
| 454 50× | 1,655,657 | 326 | 7,316 | -1.33E + 07 | 28 | 47.72 | |
| PBcR 300× | 1,877,407 | 3 | 573,021 | -1.33E + 07 | 0 | >60 | |
| S. enterica Newport | MiSeq 56× 2×150 bp 500 bp (MaSuRCA iCORN) | 5,187,269 | 114 | 195,780 | -2.24E + 07 | 360 | 41.59 |
| 454 23× + 2× 10 kbp | 5,005,089 | 172 | 372,513 | -2.25E + 07 | 39 | 51.08 | |
| PBcR 200× | 5,029,197 | 2 | 4,919,684 | -2.24E + 07 | 2 | >60 | |
Organism: the genome being assembled. Assembled with: the sequencing data used for assembly. 454 sequencing was unpaired FLX+, with paired-end sequencing available for some genomes, as indicated. MiSeq sequencing was paired-end, indicated as 2×Xbp Yb where X is the target read length and Y is the paired-end size. Column definitions are the same as in Table 2. PacBio RS sequences were self-corrected and assembled as in Table 2. 454 sequences were assembled with Newbler [39] and MiSeq sequences were assembled with SPAdes [43] and MaSuRCA [38,44]. Both assemblies were polished using iCORN [45] and the one with the best LAP score was reported.
Koren et al.
Koren et al. Genome Biology 2013 14:R101 doi:10.1186/gb-2013-14-9-r101
