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Antimicrobial Resistance

The amrfinderplus module uses AMRFinder+ to screen assemblies and proteins for antimicrobial resistance and virulence genes.

Output Overview

Below is the default output structure for the amrfinderplus step in Bactopia. Where possible the file descriptions below were modified from a tools description.

│   └── tools
│       └── amrfinderplus
│           ├── <SAMPLE_NAME>-genes.tsv
│           ├── <SAMPLE_NAME>-proteins.tsv
│           └── logs
│               ├── nf-amrfinderplus.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── amrfinderplus-<TIMESTAMP>
        ├── merged-results
        │   ├── amrfinderplus-genes.tsv
        │   ├── amrfinderplus-proteins.tsv
        │   └── logs
        │       └── amrfinderplus-{genes|proteins|-concat
        │           ├── nf-merged-results.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── amrfinderplus-report.html
            ├── amrfinderplus-timeline.html
            └── amrfinderplus-trace.txt


Merged Results

Below are results that are concatenated into a single file.

Filename Description
amrfinderplus-genes.tsv A merged TSV file with AMRFinder+ results using nucleotide inputs
amrfinderplus-proteins.tsv A merged TSV file with AMRFinder+ results using protein inputs


Below is a description of the per-sample results from AMRFinder+.

Extension Description
-genes.tsv A TSV file with AMRFinder+ results using nucleotide inputs
-proteins.tsv A TSV file with AMRFinder+ results using protein inputs

Audit Trail

Below are files that can assist you in understanding which parameters and program versions were used.


Each process that is executed will have a folder named logs. In this folder are helpful files for you to review if the need ever arises.

Extension Description
.begin An empty file used to designate the process started
.err Contains STDERR outputs from the process
.log Contains both STDERR and STDOUT outputs from the process
.out Contains STDOUT outputs from the process
.run The script Nextflow uses to stage/unstage files and queue processes based on given profile
.sh The script executed by bash for the process
.trace The Nextflow Trace report for the process
versions.yml A YAML formatted file with program versions



Parameter Description
--ident_min Minimum proportion of identical amino acids in alignment for hit (0..1)
Type: number, Default: -1
--coverage_min Minimum coverage of the reference protein (0..1)
Type: number, Default: 0.5
--organism Taxonomy group to run additional screens against
Type: string
--translation_table NCBI genetic code for translated BLAST
Type: integer, Default: 11
--amrfinder_noplus Disable running AMRFinder+ with the --plus option
Type: boolean
--report_common Report proteins common to a taxonomy group
Type: boolean
--report_all_equal Report all equally-scoring BLAST and HMM matches
Type: boolean
--amrfinder_opts Extra AMRFinder+ options in quotes.
Type: string


If you use Bactopia and amrfinderplus in your analysis, please cite the following.