Table 5.

Assembly evaluation results on aligned and recruited reads using the genomes of HBV, HCV, and HPgV as references

Align	Tool	Bowtie2 aligned			Bowtie2 Recruited
		Contig #	N50	Genome cov. (%)	Contig #	N50	Genome cov. (%)
5%	TAR-VIR	11	920	27.3	97	3643	82.3
	SGA	14	645	26.8	63	675	68.4
	SPAdes	5	1177	27.6	15	3636	79.6
	SAVAGE	13	698	21.6	49	806	40.4
10%	TAR-VIR	61	794	67.4	31	2635	84.0
	SGA	26	663	56.4	72	706	69.5
	SPAdes	15	1251	65.4	19	3373	79.3
	SAVAGE	30	631	40.6	32	915	26.5
15%	TAR-VIR	97	939	80.9	14	3579	83.1
	SGA	56	617	57.7	74	722	70.2
	SPAdes	20	1689	77.6	16	3986	81.0
	SAVAGE	32	639	29.9	24	999	27.6
20%	TAR-VIR	38	1852	84.5	77	5678	86.4
	SGA	78	661	59.5	374	537	64.5
	SPAdes	23	2,710	83.8	10	4830	84.6
	SAVAGE	19	671	19.1	15	823	5.5

‘cov.’ is the abbreviation for ‘coverage’. The default assembly component in TAR-VIR is PEHaplo