A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

Table 1

The performances of assembling different kinds of repeats.

Sequence (Containing)	Repeat			Contigs (kb)		Accuracy (%)			Genome coverage (%)
	TRC	CNRC	NNC	N50	Max	CN-accuracy	Rep-accuracy	C-accuracy
Interspersed repeats	6	3, 6, 8, 5, 10, 8	73	9.1	26	100	99.9	100	100.9
Tandem repeats	6	6, 18, 9, 4, 20, 9	51	13.2	31.3	100	99.8	100	101
Compound repeats	12	Appendix	110	13.9	32.9	100	99.8	100	101

Three sequences with length 𝐿=500 kb, 500 kb, and 1 Mb containing different types of repeats. Contigs of repeat and nonrepeat are generated independently by SWA with basic parameters: read length 𝐿_𝑟=50, filtered times = 1, sliding window size 𝐿_𝑤=3, and 𝑘-mer=10. Contigs smaller than 200 are removed.