Comparison of the performance of an amplicon sequencing assay based on Oxford Nanopore technology to real-time PCR assays for detecting bacterial biodefense pathogens

Table 3 Detailed PCR assay information

Organism	Strain(s)	PCR Assay ID_Number	Molecule Lengths (bp)				Probe Dye /Channel	Quencher	PCR Plex
Organism	Strain(s)	PCR Assay ID_Number	Forward Primer	Probe	Reverse Primer	Amplicon	Probe Dye /Channel	Quencher	PCR Plex
B. anthracis	708	PRC_01	29	30	26	110	FAM	QSY (3′)	3
B. anthracis	708	PRC_04	20	27	20	182	VIC	QSY (3′)
B. anthracis	708	PRC_07	21	31	20	96	NED	QSY (3′)
Y. pestis	113,114	PRC_09	19	25	22	68	FAM	QSY (3′)	4
Y. pestis	113	PRC_11	23	30	25	79	VIC	QSY (3′)
Y. pestis	114	PRC_14	20	27	22	103	NED	QSY (3′)
Y. pestis	113,114	PRC_15	22	26	17	67	CY5	QSY (3′)
F. tularensis	239,240,241	PRC_23	30	33	25	135	FAM	QSY (3′)	4
F. tularensis	239	PRC_28	25	30	24	171	VIC	QSY (3′)
F. tularensis	240	PRC_29	30	40	27	119	NED	QSY (3′)
F. tularensis	241	PRC_30	33	25	31	126	CY5	QSY (3′)
B. mallei	164	PRC_49	24	20	20	100	FAM	QSY (3′)	3
B. pseudomallei	197	PRC_50	24	27	20	115	VIC	QSY (3′)
B. pseudomallei	197	PRC_65	18	23	19	67	NED	QSY (3′)

Probe (usage count): FAM (4), VIC (4), NED (4), CY5 (2). Organism and strains shown with matching PCR assay(s). Primer and probe lengths also presented with associated real-time PCR channels used for detection

ISSN: 1471-2164