A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

Table 7

Assemblies of S. aureus (genome size 2,903,081).

Assemblers	Repeat				Contigs (kb)					𝐸-size	Assembly size (kb)	Genome coverage (%)
	TRC	NNC	Rep-size	Rep-acc	Num.C	N90	Mean	N50	Max
SWA	30	1834	20.7 kb	82%	1864	0.8	1.6	2.5	14.4	3115	2939	100.1
ABySS	7	293	6.8 kb	30%	302	7.0	12	24.8	125	31403	3647	125.6
Allpaths-LG	3	57	2.6 kb	4.3%	60	31	47	66.2	234	90078	2869	98.8
Bambus2	6	103	7.5 kb	35%	109	11	15	16.7	158	19610	2833	97.6
MSR-CA	7	87	4.4 kb	15%	94	21	30	48.2	139	50381	2862	98.5
SGA	18	1232	19.4 kb	83.8%	1252	1.0	2.2	4.0	16.8	4712	2833	97.6
SOAPdenovo	9	98	7.5 kb	38.6%	107	35.5	27	62.7	518.7	68002	2909	100.2
Velvet	15	147	13.8 kb	39.3%	165	11.4	17.6	41.5	169	48511	2847	98

N50, N90, and mean values are based on the same genome size. The contigs are all corrected and those smaller than 200 were removed.