Table 2.

Assembly results on SARS-CoV aligned and recruited metagenomic data

Aligned	Tool	# Contigs	N50	Genomes covered (%)	Mismatch rate (%)
Bowtie2 L,0,-0.9	TAR-VIR	58	505	19.7	0.02
	SGA	56	505	20.1	0.03
	SPAdes	34	569	12.9	0.16
	SAVAGE	54	455	17.5	0.0
Recruited	Tool	# Contigs	N50	Genomes covered (%)	Mismatch rate (%)
	TAR-VIR	7	29,676	98.9	0.0
	SGA	13	26,729	98.9	0.0
	SPAdes	14	15,882	92.1	0.51
Bowtie2 L,0,-0.9	SAVAGE	22	12,445	97.0	0.0
Aligned	Tool	# Contigs	N50	Genomes covered (%)	Mismatch rate (%)
	TAR-VIR	84	1192	55.1	0.0
	SGA	85	1027	56.5	0.0
	SPAdes	67	1012	44.6	0.12
BWA B:1	SAVAGE	68	669	32.3	0.0
Recruited	Tool	# Contigs	N50	Genomes covered (%)	Mismatch rate (%)
BWA B:1	TAR-VIR	6	29,706	99.5	0.0
	SGA	18	12,638	99.5	0.0
	SPAdes	21	10,353	89.2	0.39
	SAVAGE	56	5140	89.3	0.0

The default assembly tool in TAR-VIR is PEHaplo. Definition of the metrics can be found in “Data properties and evaluation metrics” section