RGI Resistance Gene Identifier

RGI can be used to predict resistomes from protein or nucleotide data based on homology and SNP models. Analyses can be performed via this web portal (20 Mb limit), via the command line, or via use of a Galaxy wrapper. The command line version can be obtained from the Download section of the CARD website. You can additionally install RGI from Conda or run RGI from Docker.

This web portal supports analysis of genomes, genome assemblies, metagenomic contigs, or proteomes. The command line tool additionally supports analysis of metagenomic reads and k-mer prediction of pathogen-of-origin for AMR genes.

Web portal - RGI 6.0.3, CARD 3.3.0: Open Reading Frame (ORF) prediction using Prodigal, homolog detection using DIAMOND, and Strict significance based on CARD curated bitscore cut-offs. Options included for percent identity filtering, low quality/coverage assemblies, merged metagenomic reads, small plasmids or assembly contigs (<20,000 bp).

Online RGI results cached for 7 days. As the CARD curation evolves, the results of the RGI evolve. RGI targets, reference sequences, and significance cut-offs are under constant curation. Full documentation for the RGI can be found at GitHub.

Use RGI:

Enter a GenBank accession(s):

Nucleotide sequences will undergo ORF calling to generate predicted protein sequences. Examples: JN420336.1, AY123251.1, HQ451074.1, AL123456

Select Data Type:

DNA sequence Protein sequence

Upload FASTA sequence file(s):

Upload a plain text file containing DNA or protein sequence(s) in FASTA format (20 Mb limit). The file can contain more than one FASTA formatted sequence, such as assembly contigs or multiple proteins. Each file will be treated as a single sample.

Select Criteria:

Perfect and Strict hits only Perfect, Strict and Loose hits

Nudge ≥95% identity Loose hits to Strict:

Exclude nudge Include nudge

CARD:Live

Consent, allowing CARD to collect pathogen, AMR gene list, and geotemporal data for these isolates.

The CARD:Live project collects pathogen identification, MLST, AMR gene list, date, and geographical region for genome sequences submitted to RGI online, providing a dynamic view of the antibiotic resistant isolates being analyzed around the world. No sequence information is collected. Full information at CARD:Live.

Sequence Quality:

High quality/coverage¹ Low quality/coverage²

¹ Complete genomes, plasmids, or high quality assemblies (includes contigs > 20,000 bp). Excludes prediction of partial genes.
² Low quality/coverage assemblies, metagenomic merged reads, small plasmids or assembly contigs (<20,000 bp). Includes prediction of partial genes.

Upload external RGI json results and visualize:

Upload a JSON file containing RGI results generated using the command-line version. File size limited to 20 Mb. Note that only Loose hits of e-10 or better can be visualized.

Upload JSON