A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

Table 8

Assemblies of Rhodobacter sphaeroides (genome size 4,603,060).

Assemblers	Repeat				Contigs (kb)					𝐸-size	Assembly size (kb)	Genome coverage (%)
	TRC	NNC	Rep-size	Rep-acc	Num.C	N90	Mean	N50	Max
SWA	13	1774	7.8 kb	44.5%	1787	1.3	2.6	4.2	29.4	5812	4600.3	99.94
ABySS	13	1910	8.3 kb	44.5%	1915	1.1	2.5	4.2	54.7	6877	4969.5	108
Allpaths-LG	2	202	1.4 kb	6.7%	204	11.5	22.5	34.4	106	35973	4587.8	99.6
Bambus2	2	175	1.3 kb	9.2%	177	6.1	8.5	12.8	279	16281	4371.6	94.9
CABOG	1	312	0.3 kb	8.9%	322	6.5	13	17.9	88.5	21539	4238	92
MSR-CA	7	388	4.1 kb	25.4%	395	5.7	11.3	19	83.7	21579	4465	97
SGA	9	3053	3.9 kb	64.3%	3067	0.66	1.4	2.9	29.5	4067	4502.7	97
SOAPdenovo	9	195	3.7 kb	84.5%	204	7.8	11.8	14.3	376	18553	4596	99.8
Velvet	5	578	2.2 kb	24.5%	583	4.6	7.7	14.5	60.7	16711	4503	97.8

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