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

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