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

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

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