Fig. 1

A flowchart of the MGS2AMR pipeline. The MGS2AMR pipeline accepts metagenomic sequencing (MGS) data as short-read sequencing files in the FASTQ format. The MGS data is fed to MetaCherchant that makes genomic assembly using ARG sequences as seeds. The resulting raw assembly (GFA) files are subsequently processed to reconstruct the ARG and to score the assembly paths. These scores, in conjunction with the BLASTn homology search, are used to annotate the identified ARG with respect to the origin (bacterial species or plasmid). Rectangles represent data files, hexagons—software employed. File formats: FASTA, FASTQ, GFA Graphical Fragment Assembly, CSV comma-separated values