CARD-RGI

What does it do?

Use CARD-RGI to predict the resistome of bacterial isolate assemblies or raw FASTQ data using the Comprehensive Antibiotic Resistance Database and Resistance Gene Identifier.

CARD-RGI supports two analysis modes:

  • isolate — analyzes bacterial isolate sequence assemblies;
  • metagenome — analyzes metagenomic FASTQ files and can also be used to analyze isolate FASTQ files.

The Redmine metagenome workflow uses KMA to align CARD targets to raw reads. The Redmine automator does not expose the alternative BWA or Bowtie 2 aligners available in the standalone CARD-RGI software.

For background and output definitions, see the CARD website, CARD-RGI documentation, and Alcock et al. (2020). Cite the CARD authors when publishing results produced with this automator.

How do I use it?

Subject

In the Subject field, enter:

CARDRGI

Spelling matters, but matching is not case-sensitive.

Description

The Description field must contain:

  1. an analysis declaration as the first line; and
  2. one SEQID per line.

Isolate assemblies

Use analysis=isolate for bacterial isolate sequence assemblies:

analysis=isolate
2026-SEQ-0001
2026-SEQ-0002

Raw FASTQ data

Use analysis=metagenome for metagenomic FASTQ files. This mode can also force resistome analysis of isolate FASTQ files:

analysis=metagenome
2026-SEQ-0001

Attachments

The supplied documentation does not identify a required attachment for either supported analysis mode. CARD-RGI retrieves the requested sequence data using the listed SEQIDs.

Optional parameters

loosehits

Controls whether the results include CARD-RGI loose hits in addition to strict and perfect matches.

  • Default: False
  • Enable with: loosehits=TRUE

Loose hits may or may not contribute to resistance and require careful interpretation.

partialgenes

Controls whether partial gene matches are included.

  • Default: False
  • Enable with: partialgenes=TRUE

Examples

Isolate analysis

analysis=isolate
loosehits=TRUE
2026-SEQ-0001
2026-SEQ-0002

Raw-read analysis

analysis=metagenome
2026-SEQ-0001

See issue 28111 for an example CARD-RGI request. The example uses analysis=metagenome with an isolate sequence rather than a true metagenome. Temporary result-download links associated with the issue may expire.

Interpreting results

When CARD-RGI finishes, it uploads an archive named using the Redmine issue identifier:

card-rgi_output_redmineID.zip

Isolate analysis

The archive contains a combined CSV file:

CARDRGI_output.csv

This file summarizes AMR gene results for all requested sample sequences. Review the Best_Identities column, which reports the percentage identity between the sequence and its top CARD hit.

A result with 100 percent identity provides stronger evidence for the reported target, but identity alone does not establish a resistance phenotype. Efflux systems and point mutations may confer resistance only in particular genera or species. Interpret every result in its organism-specific context.

The isolate archive also contains:

  • individual result files for each sequence; and
  • an RGI heatmap file summarizing all isolate sequences in the request.

For detailed column definitions, consult the RGI main Tab-Delimited Output Details in the CARD-RGI documentation.

Metagenome analysis

The archive contains individual output files for each analyzed sequence and two combined mapping files:

CARDRGI_gene_mapping_output.csv
CARDRGI_allele_mapping_output.csv
  • CARDRGI_gene_mapping_output.csv summarizes resistance-gene results detected in the raw FASTQ data.
  • CARDRGI_allele_mapping_output.csv reports the top allele hits for each sequence.

How long does it take?

Runtime depends on the selected analysis mode, amount of sequence data, enabled options, and number of requested sequences. Expect approximately two to five minutes per sequence.

What can go wrong?

A requested SEQID is unavailable

Symptom: The Redmine issue receives a warning identifying unavailable sequences.

Likely cause: CARD-RGI cannot locate the assembly or raw FASTQ files required for the selected analysis mode.

What to do: Verify each SEQID, confirm that the required sequence-data type is available, and submit a corrected request.

The analysis mode does not match the available input

Symptom: The automator cannot locate or process the expected data for one or more SEQIDs.

Likely cause: analysis=isolate was requested for raw reads, or analysis=metagenome was requested when the intended input was an assembly.

What to do: Use analysis=isolate for bacterial isolate assemblies and analysis=metagenome for raw FASTQ data.

Loose or partial hits are overinterpreted

Symptom: A reported hit appears weak, incomplete, or inconsistent with the organism's expected resistance profile.

Likely cause: loosehits=TRUE or partialgenes=TRUE included lower-confidence or incomplete matches.

What to do: Review identity, match category, gene completeness, organism context, and CARD documentation before drawing conclusions.

  • ResFinder — use to detect acquired AMR genes in draft genome assemblies; it does not detect resistance caused by chromosomal point mutations.
  • StarAMR — combines acquired-gene detection with supported PointFinder mutation detection for Campylobacter and Salmonella assemblies.
  • KMA — use for the Redmine KMA automator's curated AMR, biocide, metal, verotoxin, or custom target databases in assemblies or raw reads.
  • PointFinder — use for supported chromosomal resistance mutations.