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WF_2_FindAMR.md

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Workflow 2 Script

Searching for Antimicrobial Resistance


WF_2_FindAMRs.py

  • find_AMR_genes()
    • Calls rrun_AMR, parse_AMR from helper file
    • Returns Dictionary of all found antimicrobial resistance

WF_2_helper.py

  • run_AMR()

    • Run antimicrobial resistance analysis against NCBI database to find resistance genes

  • parse_AMR()

    • Parses output files
    • Return Dictionary of results