A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

Table 9

Assemblies of human chromosome 14 (genome size 88,289,540).

Assemblers	Repeat				Contigs (kb)					𝐸-size	Assembly size (kb)	Genome coverage (%)
	TRC	NNC	Rep-size	Rep-acc	Num.C	N90	Mean	N50	Max
SWA	198	26824	129.3 kb	88.3%	27021	1.6	3.3	6.7	52	8737	87936	99.6
ABySS	143	51647	121.4 kb	30.1%	51924	0.7	1.7	2.0	30	3134	73341	83
Allpaths-LG	88	4441	156.7 kb	47.3%	4529	9.7	18.7	21.0	240	27157	84435	95.6
Bambus2	154	13437	293 kb	66.7%	13592	2.4	3.1	4.3	261	6345	68243	77.3
CABOG	70	3291	255 kb	39.9%	3361	13.7	21.6	23.7	296	30689	86232	97.6
MSR-CA	190	29901	526 kb	85.3%	30103	1.2	2.7	4.3	53.9	5927	83291	94.3
SGA	187	56278	283 kb	50.4%	56939	0.6	1.4	2.7	30	3737	82375	93.3
SOAPdenovo	188	21552	476 kb	73.3%	22689	1.8	4.2	7.4	141	9801	92603	104.9
Velvet	192	45294	339 kb	56.9%	45564	0.7	1.6	2.1	22.5	3049	74740	84.6

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