The following command will bring up RGI's main help menu:
rgi --help usage: rgi <command> [<args>]
commands are:
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Database
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auto_load Automatically loads CARD database, annotations and k-mer database
load Loads CARD database, annotations and k-mer database
clean Removes BLAST databases and temporary files
database Information on installed card database
galaxy Galaxy project wrapper
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Genomic
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main Runs rgi application
tab Creates a Tab-delimited from rgi results
parser Creates categorical JSON files RGI wheel visualization
heatmap Heatmap for multiple analysis
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Metagenomic
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bwt Align reads to CARD and in silico predicted allelic variants (beta)
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Baits validation
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tm Baits Melting Temperature
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Annotations
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card_annotation Create fasta files with annotations from card.json
wildcard_annotation Create fasta files with annotations from variants
baits_annotation Create fasta files with annotations from baits (experimental)
remove_duplicates Removes duplicate sequences (experimental)
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Pathogen of origin
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kmer_build Build AMR specific k-mers database used for pathogen of origin (beta)
kmer_query Query sequences against AMR k-mers database to predict pathogen of origin (beta)
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)Help screens for subcommands can be accessed using the -h argument, e.g.
rgi load -h