A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

Table 5

The effect of filtered times to SWA.

Filtered times	Repeat			Contigs (kb)		Accuracy (%)			Genome coverage (%)
	TRC	CNRC	NNC	N50	Max	CN-accuracy	Rep-accuracy	C-accuracy
1	11	Appendix	801	0.3	2.3	100	66.8	100	53.4
2	12	Appendix	418	1.8	7.6	100	82.1	100	101.9
3	13	Appendix	1025	0.3	2.3	100	68	100	77.4

Sequence length 𝐿=500 kb containing five kinds of repeats. Contigs of repeat and nonrepeat are generated in an independent way by SWA at different levels with basic parameters: sequencing depth 𝑆_𝑑=0.5, size of sliding window 𝐿_𝑤=3, read length 𝐿_𝑟=60, and 𝑘-mer=15. Contigs smaller than 200 are removed.