TABLE 5.

Practical considerations for mNGS and tNGS workflows

Step	Consideration(s) for workflow
	Metagenomic NGS	RPIP/Explify targeted NGS
Processing and library preparation	Less extensive library prepn; lower cost for library prepn kits without targeted reagents	More extensive library prepn; additional time and higher reagent cost
Sequencing	Greater depth (goal of 10 million reads/sample); higher sequencing cost per sample	Shallower depth (goal of 3 million reads/sample); lower sequencing cost per sample
Bioinformatic analysis	Open-source bioinformatics; more involved and requires bioinformatic experience and database curation/maintenance; additional resource and time cost; ability to detect more organisms for other research questions	Less involved; does not require bioinformatic experience or database management
Result interpretation	Markedly more results requiring interpretation; possible missed pathogens with abundant resident microbiota	Easier interpretation, with potential pathogens listed on Explify report (but interpretation still required)
Detectable analytes	Broadest possible within processing and database limitations	Narrower; partially limited by bioinformatic analysis process
AMR prediction	Not studied but theoretically possiblea	Achievable but requires optimization

^aSee reference 33.