Fig. 3

General overview of the NanoARG pipeline. FASTA input reads are processed by five modules to annotate reads according to ARGs, MRGs, MGEs, and other functional genes and taxonomic affiliation. Annotations are then processed through several stages to achieve the desired analysis (relative abundance, network analysis, co-occurrence, and putative pathogens). All analyses are packed into a JavaScript Object Notation (JSON) file that can be easily streamed using an http request