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This application is used to predict resistome(s) from protein or nucleotide data based on homology and SNP models. The application uses data from CARD database.

• License
• Requirements
• Install dependencies
• Install RGI from project root
• Running RGI tests
• Help menu
• Usage
• Load card.json
• Check database version
• Run RGI
• Run RGI using GNU parallel
• Running RGI with short contigs to predict partial genes
• Clean previous or old databases
• RGI Heatmap
• Run RGI from docker
• Tab-delimited results file
• Support & Bug Reports

Use or reproduction of these materials, in whole or in part, by any non-academic organization whether or not for non-commercial (including research) or commercial purposes is prohibited, except with written permission of McMaster University. Commercial uses are offered only pursuant to a written license and user fee. To obtain permission and begin the licensing process, see CARD website

• Prodigal v2.6.3
• NCBI BLAST v2.6.0+
• DIAMOND v0.8.36
• Python 3.6

• pip3 install biopython
• pip3 install filetype
• pip3 install pandas
• pip3 install pytest
• pip3 install mock

pip3 install .

or

python3 setup.py build
python3 setup.py test
python3 setup.py install

cd tests
pytest -v -rxs

rgi --help

   usage: rgi <command> [<args>]
               commands are:
               main     Runs rgi application
               tab      Creates a Tab-delimited from rgi results
               parser   Creates categorical JSON files RGI wheel visualization
               load     Loads CARD database JSON file
               clean    Removes BLAST databases and temporary files
               galaxy   Galaxy project wrapper
               database Information on installed card database
               heatmap  Heatmap for multiple analysis
               ---------------------------------------------------------------------------------------
               bwt                   Metagenomics resistomes (Experimental)
               card_annotation       Create fasta files with annotations from card.json (Experimental)
               wildcard_annotation   Create fasta files with annotations from variants (Experimental)
               baits_annotation      Create fasta files with annotations from baits (Experimental)
               remove_duplicates     Removes duplicate sequences (Experimental)
               kmer_build            Build CARD*kmer database (Experimental)
               kmer_query            Query sequences through CARD*kmers (Experimental)

Resistance Gene Identifier - <version_number>

positional arguments:
command     Subcommand to run

optional arguments:
-h, --help  show this help message and exit

Use the Resistance Gene Identifier to predict resistome(s) from protein or
nucleotide data based on homology and SNP models. Check
https://card.mcmaster.ca/download for software and data updates. Receive email
notification of monthly CARD updates via the CARD Mailing List
(https://mailman.mcmaster.ca/mailman/listinfo/card-l)

• local or working directory

  rgi load --afile /path/to/card.json --local

• system wide

  rgi load --afile /path/to/card.json

• local or working directory

  rgi database --version --local

• system wide

  rgi database --version

• local or working directory

  rgi main --input_sequence /path/to/protein_input.fasta --output_file /path/to/output_file --input_type protein --local

• system wide

  rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file --input_type contig

• system wide and writing log files for each input file. (Note add code below to script.sh then run with ./script.sh /path/to/input_files)

  #!/bin/bash
  DIR=`find . -mindepth 1 -type d`
  for D in $DIR; do
        NAME=$(basename $D);
        parallel --no-notice --progress -j+0 'rgi main -i {} -o {.} -n 16 -a diamond --clean --debug > {.}.log 2>&1' ::: $NAME/*.{fa,fasta};
  done

• local or working directory

  rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file --local --low_quality

• system wide

  rgi main --input_sequence /path/to/nucleotide_input.fasta --output_file /path/to/output_file --low_quality

• local or working directory

  rgi clean --local

• system wide

  rgi clean

• Default Heatmap

  rgi heatmap --input /path/to/rgi_results_json_files_directory/

• Heatmap with AMR Gene Family categorization

  rgi heatmap --input /path/to/rgi_results_json_files_directory/ --category gene_family

• Heatmap with AMR Gene Family categorization and fill display

  rgi heatmap --input /path/to/rgi_results_json_files_directory/ --category gene_family --display fill

• Heatmap with AMR Gene Family categorization and coloured y-axis labels display

  rgi heatmap --input /path/to/rgi_results_json_files_directory/ --category gene_family --display text

• Heatmap with frequency display enabled

  rgi heatmap --input /path/to/rgi_results_json_files_directory/ --frequency

• Heatmap with drug class category and frequency enabled

  rgi heatmap --input /path/to/rgi_results_json_files_directory/ --category drug_class --frequency --display text

• Heatmap with samples and genes clustered

  rgi heatmap --input /path/to/rgi_results_json_files_directory/ --cluster both

• Heatmap with resistance mechanism categorization and clustered samples

  rgi heatmap --input /path/to/rgi_results_json_files_directory/ --cluster samples --category resistance_mechanism --display fill

• First you you must either pull the docker container from dockerhub (latest CARD version automatically installed)

  docker pull finlaymaguire/rgi

• Or Alternatively, build it locally from the Dockerfile (latest CARD version automatically installed)

  git clone https://github.com/arpcard/rgi
  docker build -t arpcard/rgi rgi

• Then you can either run interactively (mounting a local directory called rgi_data in your current directory to /data/ within the container

  docker run -i -v $PWD/rgi_data:/data -t arpcard/rgi bash

• Or you can directly run the container as an executable with $RGI_ARGS being any of the commands described above. Remember paths to input and outputs files are relative to the container (i.e. /data/ if mounted as above).

  docker run -v $PWD/rgi_data:/data arpcard/rgi $RGI_ARGS

SNPs_in_Best_Hit_ARO

Other_SNPs

Percentage Length of Reference Sequence

Please log an issue on github issue.

You can email the CARD curators or developers directly at [email protected], via Twitter at @arpcard.