Facile, High Quality Sequencing of Bacterial Genomes from Small Amounts of DNA

Table 1

Comparison of gap counts by organism, replicon, and library preparation method. Input DNA amount for each sample follows the name of the library preparation method.

Gap counts for E. coli genome
Library preparation method-DNA input	Reference	Replicon length, bp	Cutoff based on average coverage
			0	1%	10%
NEBNext-100 ng	Plasmid 1	109,274	0	0	24
	Plasmid 2	74,213	45	145	318
	Plasmid 3	1,549	0	0	8
	Chromosome	5,253,138	26	206	1262
TruSeq-1000 ng	Plasmid	109,274	0	1	49
	Plasmid	74,213	44	200	491
	Plasmid	1,549	0	0	25
	Chromosome	5,253,138	23	449	2833
Gap counts for B. thailandensis A genome
Library preparation method-DNA input	Reference	Replicon length, bp	Cutoff based on average coverage
			0	1%	10%
NEBNext-10 ng	Chromosome 1	3,805,980	47	72	329
	Chromosome 2	2,870,750	86	125	498
NEBNext-100 ng	Chromosome 1	3,805,980	3	35	669
	Chromosome 2	2,870,750	78	151	1625
TruSeq-1000 ng	Chromosome 1	3,805,980	0	153	2747
	Chromosome 2	2,870,750	30	135	1937
Gap counts for B. thailandensis B genome
Library preparation method-DNA input	Reference	Replicon length, bp	Cutoff based on average coverage
			0	1%	10%
NEBNext-10 ng	Chromosome 1	3,805,980	37	158	1297
	Chromosome 2	2,870,750	19	38	717
NEBNext-100 ng	Chromosome 1	3,805,980	0	0	0
	Chromosome 2	2,870,750	6	158	2328
TruSeq-1000 ng	Chromosome 1	3,805,980	0	114	1874
	Chromosome 2	2,870,750	0	28	1177