Table 2.

Evaluating the short-read only assemblies

Assembler	Data type	kmer	Approx. coverage	Avg identity	Indels < 5 bp	Indels > = 5 bp	Inversions	Unalignable contigs	Relocations	SNPs
Velvet	MiSeq	59	100X	99.99	13	38	2	0	16	42
		59	75X	99.99	23	31	0	0	12	110
		59	50X	99.99	18	36	1	0	17	88
		59	25X	99.99	36	129	0	0	8	96
Ray	MiSeq	36	100X	100	1	6	2	19	2	9
		36	75X	99.99	5	10	0	11	2	35
		36	50X	99.99	2	3	0	8	2	26
		36	25X	100	5	5	1	4	4	41
	Ion	29	100X	99.86	5645	29	0	4	1	67
		29	75X	99.9	4209	14	0	4	1	58
		29	50X	99.93	2784	7	0	0	0	58
		29	25X	99.95	1933	3	0	1	1	54
MIRA	MiSeq	n/a	100X	99.99	8	6	13	2	15	73
		n/a	75X	99.99	20	4	11	0	11	124
		n/a	50X	99.99	31	5	15	0	9	113
		n/a	25X	99.99	9	7	7	0	7	81
	Ion	n/a	100X	99.98	207	6	11	4	11	50
		n/a	75X	99.98	239	8	14	2	9	42
		n/a	50X	99.98	292	10	9	1	8	58
		n/a	25X	99.98	524	10	9	0	3	34

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