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 5 Read count ranges for first 10 min and full 48 h of sequencing data

Run Time	Preprocessing	Sample Count	Group	Read Counts
Run Time	Preprocessing	Sample Count	Group	min	max	median
10 Minutes	Adapter + Quality trimmed	405	all samples	0	11,013	178
		405	mapped per sample	0	1697	27
		5670	mapped per assay	0	1502	0
		1129	mapped per assay (zeros removed)	1	1502	80
48 Hours	Adapter + Quality trimmed	405	all samples	0	4,322,566	67,717
		405	mapped per sample	0	579,930	10,803
		5670	mapped per assay	0	472,720	0
		1561	mapped per assay (zeros removed)	1	472,720	346

Mapped in this table refers to amplicon mapped. Note that for the ‘mapped per assay’ group, the median value includes counts for assays that should remain at zero, i.e. are true negatives

ISSN: 1471-2164