. 2024 Mar 7;12(4):e03885-23. doi: 10.1128/spectrum.03885-23

TABLE 1.

Bioinformatic analysis and QC metrics used for sequence data from each WCBL project

WCBL project	Bioinformatic platform used	QC metrics used
WCBL project	Bioinformatic platform used	Coverage	Average quality (Q score)	Assembly sequence length	Contigs	Scaffolds	% core genome
ARLN	In-house-developed pipeline	Yes^c	Yes^d	Yes^e	No	Yes^g	No
GT	GalaxyTrakr, MicroRunQC	Yes^a^,e	Yes^d	Yes^a^,e	Yes^a^,e	No	No
EIP	BioNumerics7.6	Yes^b^,e	Yes^d	Yes^b^,e	Yes^b^,e	No	Yes^b^,e
HAI	In-house-developed pipeline	Yes^c	Yes^d	Yes^e	No	Yes^g	No
RES	In-house-developed pipeline	Yes^c	Yes^d	Yes^e	No	Yes^g	No
PPP	In-house-developed pipeline	Yes^c	Yes^d	Yes^e	No	Yes^g	No
PN	BioNumerics7.6	Yes^b^,e	Yes^d	Yes^b^,e	Yes^b^,e	No	Yes^b^,e
RFS	BioNumerics7.6	Yes^b^,e	Yes^d	Yes^b^,e	Yes^b^,e	No	Yes^b^,e
LEG	In-house-developed pipeline	Yes^c	Yes^d	Yes^b^,e	Yes^f	No	No

^{^a}

(12).

^{^b}

^{^c}

All data must have ≥40X× coverage.

^{^d}

All projects require average Q score ≥ 30.

^{^e}

Organism dependent.

^{^f}

(13).

^{^g}

All assemblies must produce ≤500 scaffolds. RFS, Retail Food Study; ARLN, AR Lab Network.