Reducing assembly complexity of microbial genomes with single-molecule sequencing

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.

ISSN: 1474-760X