A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

Table 3

The effect of read length to SWA.

Read length	Repeat			Contigs (kb)		Accuracy (%)			Genome coverage (%)
	TRC	CNRC	NNC	N50	Max	CN-accuracy	Rep-accuracy	C-accuracy
36	10	Appendix	33	19	34	100	98.2	100	100.1
50	9	Appendix	23	19	48	100	99	100	100.3
101	7	3, 4, 6, 5, 2, 2, 2	21	19.1	48.1	100	99.2	100	100.8
150	6	3, 4, 2, 6, 5, 2	22	19.3	48.3	100	99.6	100	101

Sequence length 𝐿=500 kb containing five types of repeats. Read length is changing from 36 to 150. Contigs of repeat and nonrepeat are generated in an independent ways by SWA at different levels with basic parameters: sequencing depth 𝑆_𝑑=4, filtered times = 1, sliding window size 𝐿_𝑤=3, and 𝑘-mer=10. Contigs smaller than 200 are removed.