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PathoFact will generate a number of different reports within the PathoFact_report directory, dependent on which module has been run:
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PathoFact will generate a number of different reports within the PathoFact_report directory, dependent on which module has been run:
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1. AMR_MGE_prediction_{sample}_report.tsv (AMR)
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1. AMR_MGE_prediction_{sample}_report.tsv **(AMR)**
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2. Virulence_prediction_{sample}_report.tsv (vir)
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2. Virulence_prediction_{sample}_report.tsv **(Vir)**
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3. Toxin_prediction_{sample}_report.tsv (tox)
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3. Toxin_prediction_{sample}_report.tsv **(Tox)**
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4. Toxin_gene_library_{sample}_report.tsv (tox)
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4. Toxin_gene_library_{sample}_report.tsv **(Tox)**
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5. PathoFact_{sample}_predictions.tsv (complete)
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5. PathoFact_{sample}_predictions.tsv **(complete)**
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