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rgi

Tags: bacteria antibiotic-resistance card resistance-genes bactopia-tool

Prediction of antibiotic resistance genes using RGI.

This Bactopia Tool uses Resistance Gene Identifier (RGI) to identify and characterize antibiotic resistance genes in bacterial assemblies. RGI integrates with the Comprehensive Antibiotic Resistance Database (CARD) to provide high-confidence predictions of resistance determinants, including perfect and strict hits to known resistance genes, as well as loose hits for novel variants. The tool generates detailed reports in both JSON and TSV formats, along with heatmap visualizations for comparative analysis across multiple samples.

Usage​

Bactopia CLI:

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

Nextflow:

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

Outputs​

Expected Output Files​

<BACTOPIA_DIR>
├── <SAMPLE_NAME>
│   └── tools
│       └── rgi_main
│           ├── <SAMPLE_NAME>.json
│           ├── <SAMPLE_NAME>.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
├── GCF_900478275
│   └── tools
│       └── rgi_main
│           ├── GCF_900478275.json
│           ├── GCF_900478275.tsv
│           └── logs
│               ├── nf.command.{begin,err,log,out,run,sh,trace}
│               └── versions.yml
└── bactopia-runs
    └── rgi-<TIMESTAMP>
        ├── merged-results
        │   ├── logs
        │   │   └── rgi-concat
        │   │       ├── nf.command.{begin,err,log,out,run,sh,trace}
        │   │       └── versions.yml
        │   └── rgi.tsv
        ├── nf-reports
        │   ├── rgi-dag.dot
        │   ├── rgi-report.html
        │   └── rgi-timeline.html
        └── rgi-heatmap
            ├── logs
            │   └── rgi-heatmap
            │       ├── nf.command.{begin,err,log,out,run,sh,trace}
            │       └── versions.yml
            ├── rgi-2.csv
            ├── rgi-2.eps
            └── rgi-2.png

Per-Sample Results​

FileDescription
*.jsonJSON report containing detailed RGI results for each sample
*.txtTab-delimited report of RGI results for each sample

Merged Results​

FileDescription
rgi.tsvMerged TSV file containing RGI results from all samples
rgi-2.{csv,png}Heatmap representations of resistance genes across 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
rgi-dag.dotThe Nextflow DAG visualization
rgi-report.htmlThe Nextflow Execution Report
rgi-timeline.htmlThe Nextflow Timeline Report
rgi-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

RGI Main Parameters​

ParameterTypeDefaultDescription
--rgi_use_diamondbooleanfalseUse DIAMOND for alignments instead of BLAST
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:

  • rgi - Predict antimicrobial resistance from protein or nucleotide data.

Citations​

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

Source​

View source on GitHub