Table 2. The number of reads assigned to species within the genera Salmonella and Listeria and the number of samples ‘positive’ for each.

Results are those obtained using default parameter settings and the Greengenes database.

Taxon	Classifier	Number of reads classified	Number of ‘positive’ samples
Listeria fleischmanniia	BLAST	7	7
	RDP	0	0
	SORTMERNA	0	0
	UCLUST	0	0
Listeria grayia	BLAST	85	39
	RDP	0	0
	SORTMERNA	4	4
	UCLUST	6	6
Listeria monocytogenes	BLAST	1	1
	RDP	0	0
	SORTMERNA	0	0
	UCLUST	0	0
Listeria weihenstephanensisa	BLAST	3,753	426
	RDP	80	54
	SORTMERNA	14	12
	UCLUST	9	8
Salmonella enterica	BLAST	457	204
	RDP	72	57
	SORTMERNA	43	40
	UCLUST	2,090	522

Notes.

^aNon-pathogenic and non-hemolytic.