A comprehensive evaluation of assembly scaffolding tools

Table 4 Results summary of genome scale data

Scaffolder	Read mapper	S. aureus			P. falciparum			Human chromosome 14
		% Correct joins found	% Joins incorrect	Score	% Correct joins found	% Joins incorrect	Score	% Correct joins found	% Joins incorrect	Score
ABySS	abyss-map	59.3	2.0	0.87	61.5	1.2	0.85	47.1	0.5	0.83
Bambus2	Bowtie 2	56.9	2.1	0.82	NA^a	NA^a	NA^a	51.6	1.5	0.72
Bambus2	BWA	57.5	0.0	0.86	NA^a	NA^a	NA^a	54.0	2.1	0.69
MIP	Bowtie -v 0	1.2	0.0	0.82	89.8	4.0	0.75	34.5	4.7	0.43
	Bowtie -v 3	0.0	NA	0.82	89.3	4.8	0.68	42.8	7.5	0.10
	Bowtie 2	0.0	NA	0.82	86.9	6.0	0.65	NA^a	NA^a	NA^a
	BWA	0.0	NA	0.82	86.0	8.0	0.42	NA^a	NA^a	NA^a
Opera	Bowtie	67.1	8.9	0.65	69.2	2.7	0.74	64.5	0.4	0.88
Opera	BWA	64.7	12.2	0.56	69.1	3.0	0.72	63.9	1.1	0.84
SCARPA	Bowtie -v 0	50.3	8.7	0.72	79.6	4.7	0.39	52.8	1.4	0.80
	Bowtie -v 3	49.1	10.9	0.31	80.8	4.5	0.41	52.6	1.4	0.80
	Bowtie 2	46.1	17.2	0.53	78.9	4.8	0.39	53.7	1.5	0.79
	BWA	46.7	7.1	0.77	79.7	4.8	0.40	53.6	1.4	0.80
SGA	Bowtie 2	49.7	1.2	0.88	52.8	0.9	0.80	49.0	0.0	0.85
SGA	BWA	43.1	1.4	0.88	51.1	5.2	0.65	41.1	0.4	0.82
SOAP2	SOAP2	78.4	8.4	0.68	64.3	3.7	0.76	79.0	2.4	0.80
SOPRA	Bowtie -v 0	53.3	2.2	0.85	87.5	0.8	0.97	66.1	0.4	0.90
	Bowtie -v 3	41.3	4.2	0.80	83.6	0.8	0.95	52.3	2.2	0.74
	Bowtie 2	24.0	4.8	0.80	75.4	0.8	0.91	NA^a	NA^a	NA^a
	BWA	25.1	6.7	0.77	81.5	0.6	0.95	NA^a	NA^a	NA^a
SSPACE	Bowtie -v 0	65.9	7.6	0.72	63.0	1.4	0.85	44.0	0.3	0.83
	Bowtie -v 3	62.9	11.0	0.62	63.3	2.0	0.83	46.4	0.4	0.84

^aData not available because scaffolder required more than 30 GB of memory or did not finish within 12 days.

ISSN: 1474-760X