A De Novo Genome Assembly Algorithm for Repeats and Nonrepeats

Table 2

The effect of depth to SWA.

Sequencing depth	Repeat			Contigs (kb)		Accuracy (%)			Genome coverage (%)
	TRC	CNRC	NNC	N50	Max	CN-accuracy	Rep-accuracy	C-accuracy
6	5	3, 4, 2, 6, 5	21	19	48	100	99.9	100	100.4
4	5	3, 4, 6, 5, 2	25	19	48	100	99.9	100	100.4
2	9	Appendix	100	7.2	20.8	100	89.2	100	101.1
1	15	Appendix	323	2.1	11.8	100	86.7	100	101.9
0.5	14	Appendix	950	0.3	3.0	100	66.7	100	63.3
0.2	17	Appendix	54	0.2	1.0	80	56.7	100	8.3

Sequence length 𝐿=500 kb containing five types of repeats. Sequencing depths are changing from 6 to 0.2. Contigs of repeat and nonrepeat are generated in an independent ways by SWA at different depths with basic parameters: read length 𝐿_𝑟=60, filtered times = 1, sliding window size 𝐿_𝑤=3, and 𝑘-mer=10. Contigs smaller than 200 are removed.