Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

Table 1 Flow cell run data

Exp/sample	Flow cell #	Run #	# of active pores	Run time (min)	Total reads	Pass reads	Fail reads	Pass/fail rate	Target virus	# of aligned reads	Avg read length [range] (bp)	Avg read error rate^a
Chik1	1	First run	345	138	19,452	5,139	14,313	35.9 %	CHIKV	556	455 [126–1477]	20.6 % (8–49 %)
Ebola1	1	First run	105	1022	13,090	1,831	11,259	16.3 %	EBOV	41	358 [220–672]	22.0 % (12–43 %)
HepC1	2	First run	171	122	10,305	729	9,877	7.4 %	HCV	6	572 [318–792]	33.1 % (24–46 %)
HepC1	2	Reload #1	293	192	26,626	2,155	25,758	8.4 %	HCV
HepC1	2	Reload #2	256	298	32,212	1,207	31,289	3.9 %	HCV
HepC1	2	Reload #3	214	156	14,805	287	14,275	2.0 %	HCV
Ebola2	3	First run	397	79	28,651	1,537	27,114	5.7 %	EBOV	593	456 [189–1430]	22.3 % (8–48 %)
Ebola2	3	Reload #1	426	222	95,861	2,899	92,962	3.1 %	EBOV
Ebola2	3	Reload #2	380	1091	166,524	1,539	164,985	0.9 %	EBOV
Ebola2	3	Reload #3	200	1357	44,272	34	44,238	0.1 %	EBOV
TOTAL					451,798	17,357	436,070	4.0 %			452 [126–1477]	24.3 % (8–49 %)

Expexperiment, CHIKV chikungunya virus, EBOV Ebola virus, HCV, hepatitis C virus
^aBased on average pairwise identity of aligned viral reads to the most closely matched reference sequence

ISSN: 1756-994X