Fig. 1

Simplified overview of a metagenomics workflow, which is broken down into two main steps. Sample collection, nucleic acid extraction, library preparation, and sequencing are depicted in the orange panel. Once reads are sequenced, data are fed into a bioinformatics pipeline (blue panel) for quality control, host subtraction, and taxonomic alignment, followed by identification and quantification of microbial species, and functional analysis. Two possible analyses are depicted and consist of pathogen detection and disease classification (figures adapted from Kalantar et al. [16]). Created with BioRender.com