Reducing assembly complexity of microbial genomes with single-molecule sequencing

Table 4 E. coli correctness on GAGE metrics

Organism	Assembled by	Number of contigs	N50	Number of structural differences	Number of discordant bases	QV	Number of indels > 5 bp
E. coli K12	MiSeq 100×	139	113,852	1	59	49.00	4
	454 50×	93	117,490	2	26	52.45	0
	MiSeq 100× + 200× CLR	2	2,367,319	2	11	56.26	2
	454 50× + 200× CLR	1	4,649,004	2	11	56.26	2
	CCS 25X + 200× CLR	1	4,653,267	0	14	55.22	2
	200× CLR	1	4,653,486	0	14	55.22	2

Organism: the genome being assembled. Assembled by: the short-read data used for correction and/or assembly. Number of contigs: the number of contigs comprising the assembly. N50: N such that 50% of the genome is contained in contigs of length ≥N. Number of structural differences: the sum of inversions, relocations, and translocations versus the reference using GAGE metrics [37]. Number of discordant bases: total number of different bases when compared to the reference. QV: estimated from the number of indels and SNPs as ${log}_{10} (\frac{assembly length}{# incorrect bases}) * 10$ . Indels >5 bp: the number of indels >5 bp reported by GAGE metrics [37]. Assemblies were generated as in Tables 2 and 3.

ISSN: 1474-760X