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amr_gene_detection

Antimicrobial resistance gene detection from assembled bacterial genomes

  • Author(s):
  • ABRomics
  • abromics-consortium
  • Pierre Marin
  • Clea Siguret
  • Release: 1.1.4
  • License: GPL-3.0-or-later
  • UniqueID: dfcedd6a-9dc1-4dcd-8b15-dbd21482f463

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