AMR gene detection workflow in an assembled bacterial genome (v1.0)

This workflow uses assembled bacterial genome fasta files (but can be any fasta file) and executes the following steps:

1. Genomic detection
   • Antimicrobial resistance gene identification:
     • staramr to blast against ResFinder and PlasmidFinder database
     • AMRFinderPlus to find antimicrobial resistance genes and point mutations
   • Virulence gene identification:
     • ABRicate with VFDB_A database
2. Aggregating outputs into a single JSON file
   • ToolDistillator to extract and aggregate information from different tool outputs to JSON parsable files

Inputs

1. Assembled bacterial genome in fasta format.

Outputs

1. Genomic detection
   • Antimicrobial resistance gene identification:
     • AMR gene list
     • MLST typing
     • Plasmid gene identification
     • Blast hits
     • AMR gene fasta (assembled nucleotide sequences)
     • Point mutation list
   • Virulence gene identification:
     • Gene identification in tabular format
2. Aggregating outputs:
   • JSON file with information about the outputs of staramr, AMRFinderPlus, ABRicate