A comprehensive evaluation of assembly scaffolding tools

Table 2 Summary of datasets

Dataset	Size (Mb)	%GC	Potential joins	Number of reads (millions)	Read length	Insert size^a	Percent reads mapped (fwd/rev)								Maximum read coverage
							Bowtie -v 0		Bowtie -v 3		Bowtie2		BWA
S. aureus perfect	2.8	32	27	0.76	76	505	96	96	95	95	97	97	97	97	40
			27	0.76	76	2,795	96	96	95	95	97	97	97	97	40
			940	0.76	76	505	95	94	94	94	96	96	96	96	40
			940	0.76	76	2,995	95	94	94	94	97	96	96	96	40
S. aureus GAGE	2.9	32	167	3.5	37	3,385	35	35	56	54	55	54	53	52	49
R. sphaeroides GAGE	4.6	68	570	2.1	101	3,695	17	11	36	32	69	68	35	30	62
P. falciparum 3D7 de novo	23.3	19	9,302	52.5	76	645	70	67	73	70	79	77	76	74	267
P. falciparum 3D7 de novo	23.3	19	9,302	12.0	75	2,705	27	25	31	30	43	42	33	32	33
Human chromosome 14 GAGE^b	88.2	40	19,935	22.7	101	2,865	46	19	68	29	90	55	69	30	38
			19,935	2.4	57-82	34,500	47	6	73	48	93	85	79	56	3

ISSN: 1474-760X