Efficient and accurate whole genome assembly and methylome profiling of E. coli

BMC Genomics

Table 1 Short read only assembly statistics

Assembler	Data type	kmer	Approx. coverage	# Contigs	% Contigs>500	Max contig size	N50	Dup-mer 21	Assembly size	% Assembly size
Velvet	MiSeq	59	100X	154	54.55%	430066	119241	0.28	4493252	98.56%
		59	75X	156	53.21%	413653	119171	0.30	4493894	98.57%
		59	50X	144	55.56%	415116	118491	0.28	4493686	98.57%
		59	25X	244	68.03%	212504	48994	0.26	4494206	98.58%
Ray	MiSeq	36	100X	93	78.49%	332975	111161	1.67	4565040	100.13%
		36	75X	90	85.56%	350117	111227	0.47	4550209	99.81%
		36	50X	100	90.00%	213879	86298	0.45	4495395	98.61%
		36	25X	292	93.15%	79672	26198	0.5	4499709	98.70%
	Ion	29	100X	734	88.56%	34241	10008	2.34	4545446	99.70%
		29	75X	578	87.02%	58878	13621	1.64	4493104	98.56%
		29	50X	440	85.00%	85800	18468	1.01	4499305	98.69%
		29	25X	415	86.51%	75474	19997	0.36	4470372	98.06%
MIRA	MiSeq	n/a	100X	1260	6.51%	388423	115369	2.16	4754899	104.30%
		n/a	75X	457	22.98%	284700	96674	0.85	4630082	101.56%
		n/a	50X	321	51.09%	221854	48362	1.01	4589987	100.68%
		n/a	25X	1071	74.51%	33745	8703	1.31	4545144	99.70%
	Ion	n/a	100X	697	10.33%	493665	180738	2.34	4763496	104.49%
		n/a	75X	429	19.58%	401639	128626	1.60	4674816	102.54%
		n/a	50X	221	37.10%	351325	144583	1.03	4598473	100.87%
		n/a	25X	153	62.75%	281400	106822	0.73	4559337	100.01%

The bolded assemblies represent the best assembly for the specified combination of sequencer and software.

ISSN: 1471-2164