Optimizing open data to support one health: best practices to ensure interoperability of genomic data from bacterial pathogens

Table 1 Quality control threshold guidelines for enterica pathogens collected for GenomeTrakr

Quality metric	Salmonella enterica	Listeria monocytogenes	Escherichia coli	Shigella sp.	Campylobacter jejuni	Vibrio parahaemolyticus
Average read quality Q score for R1 and R2	> = 30	> = 30	> = 30	> = 30	> = 30	> = 30
Average coverage	> = 30X	> = 20X	> = 40X	> = 40X	> = 20X	> = 40X
De novo assembly: Seq. length (Mbp)	~ 4.3–5.2	~ 2.7–3.2	~ 4.5–5.9	~ 4.0–5.0	~ 1.5–1.9	~ 4.8–5.5
De novo assembly: no. contigs	<=300	<=300	<=500	<=650	<=300	<=300

ISSN: 2524-4655