Table 4.

Evaluation of hybrid scaffolding assemblies

Original assembler	Original data type	Original coverage	Approx. PacBio coverage	Avg identity	Indels < 5 bp	Indels > = 5	Inversions	Missing assembly contigs	Relocation	SNPs
Velvet	MiSeq	75X	25X	99.98	416	36	4	0	31	93
			55X	99.98	471	47	3	0	25	107
			110X	99.98	299	49	2	0	24	88
Ray	MiSeq	50X	25X	99.99	191	10	3	19	3	16
			55X	99.99	210	10	2	19	2	33
			110X	99.99	185	13	3	19	2	33
	Ion	25X	25X	99.95	2092	244	8	1	39	65
			55X	99.93	3000	93	3	1	13	206
			110X	99.93	2732	79	0	1	20	171
MIRA	MiSeq	50X	25X	99.98	199	23	18	0	14	138
			55X	99.98	140	18	19	0	17	103
			110X	99.98	90	17	21	0	19	92
	Ion	25X	25X	99.97	682	14	12	0	9	59
			55X	99.97	650	14	12	0	11	92
			110X	99.97	648	19	13	0	11	74