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abritamr

Tags: bacteria antimicrobial-resistance virulence amr nata bactopia-tool

A NATA accredited tool for reporting the presence of antimicrobial resistance genes.

This Bactopia Tool uses abriTAMR to identify antimicrobial resistance genes in bacterial genomes. It runs AMRFinderPlus on each sample and collates the results into functional classes, producing detailed reports on resistance genes, partial matches, and virulence factors. It is accredited by NATA for use in reporting presence of reportable AMR genes in Victoria, Australia.

Usage​

Bactopia CLI:

bactopia --wf abritamr \
  --bactopia /path/to/your/bactopia/results

Nextflow:

nextflow run bactopia/bactopia/workflows/bactopia-tools/abritamr/main.nf \
  --bactopia /path/to/your/bactopia/results

Outputs​

Expected Output Files​

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── abritamr-<TIMESTAMP>
│           ├── <SAMPLE_NAME>.abritamr.tsv
│           ├── <SAMPLE_NAME>.amrfinder.out
│           ├── <SAMPLE_NAME>.summary_matches.tsv
│           ├── <SAMPLE_NAME>.summary_partials.tsv
│           ├── <SAMPLE_NAME>.summary_virulence.tsv
│           └── logs
│               ├── abritamr.log
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               ├── update_abritamr_db.log
│               └── versions.yml
└── bactopia-runs
    └── abritamr-<TIMESTAMP>
        ├── merged-results
        │   ├── abritamr.tsv
        │   └── logs
        │       └── abritamr-concat
        │           ├── nf.command.{begin,err,log,out,run,sh,trace}
        │           └── versions.yml
        └── nf-reports
            ├── abritamr-dag.dot
            ├── abritamr-report.html
            └── abritamr-timeline.html

Per-Sample Results​

FileDescription
*.abritamr.txtTab-delimited file combining non-empty summary files from abriTAMR
*.amrfinder.outRaw output from AMRFinderPlus (per sequence)
*.summary_matches.txtTab-delimited file with AMR gene matches per sequence
*.summary_partials.txtTab-delimited file with partial AMR gene matches
*.summary_virulence.txtTab-delimited file with virulence gene classifications

Merged Results​

FileDescription
abritamr.tsvMerged TSV file containing AMR summaries from all samples

Audit Trail​

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

Logs​

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.

ExtensionDescription
.beginAn empty file used to designate the process started
.errContains STDERR outputs from the process
.logContains both STDERR and STDOUT outputs from the process
.outContains STDOUT outputs from the process
.runThe script Nextflow uses to stage/unstage files and queue processes based on given profile
.shThe script executed by bash for the process
.traceThe Nextflow trace report for the process
versions.ymlA YAML formatted file with program versions

Nextflow Reports​

These Nextflow reports provide great a great summary of your run. These can be used to optimize resource usage and estimate expected costs if using cloud platforms.

FilenameDescription
abritamr-dag.dotThe Nextflow DAG visualization
abritamr-report.htmlThe Nextflow Execution Report
abritamr-timeline.htmlThe Nextflow Timeline Report
abritamr-trace.txtThe Nextflow Trace report

Parameters​

Required Parameters​

Define where the pipeline should find input data and save output data.

ParameterTypeDefaultDescription
--bactopiastringThe path to bactopia results to use as inputs

abriTAMR Parameters​

ParameterTypeDefaultDescription
--abritamr_speciesstringUse species specific point mutations, must provide a valid species
--abritamr_identityintegerMinimum identity of matches with amrfinder (0 - 1.0), defaults to amrfinder preset
Filtering Parameters

Use these parameters to specify which samples to include or exclude.

ParameterTypeDefaultDescription
--includestringA text file containing sample names (one per line) to include from the analysis
--excludestringA text file containing sample names (one per line) to exclude from the analysis
Optional Parameters

These optional parameters can be useful in certain settings.

ParameterTypeDefaultDescription
--outdirstringbactopiaBase directory to write results to
Nextflow Profile Parameters

Parameters to fine-tune your Nextflow setup.

ParameterTypeDefaultDescription
--datasets_cachestring<HOME>/.bactopia/datasetsDirectory where downloaded datasets should be stored.
Helpful Parameters

Uncommonly used parameters that might be useful.

ParameterTypeDefaultDescription
--wfstringbactopiaSpecify which workflow or Bactopia Tool to execute
--list_wfsbooleanList the available workflows and Bactopia Tools to use with '--wf'
--help_allbooleanAn alias for --help --show_hidden_params
--versionbooleanDisplay version text.

Composition​

This workflow uses the following subworkflows:

  • abritamr - Identify antimicrobial resistance genes using AMRFinderPlus.

Citations​

If you use this in your analysis, please cite the following.

Source​

View source on GitHub