ResFinder

What does it do?

Use ResFinder to detect acquired antibiotic-resistance genes in draft genome assemblies.

The Redmine ResFinder automator detects acquired resistance genes, which are often plasmid-borne. It does not detect resistance caused by chromosomal point mutations. For supported mutation detection, use PointFinder, StarAMR, or CARD-RGI, depending on the organism, input type, and desired analysis.

ResFinder was developed by the Danish Center for Genomic Epidemiology.

How do I use it?

Subject

In the Subject field, enter:

ResFinder

Spelling matters, but matching is not case-sensitive.

Description

In the Description field, enter one SEQID per line:

2026-SEQ-0001
2026-SEQ-0002

The requested SEQIDs must have draft genome assemblies available.

Attachments

No attachment is required. ResFinder retrieves the draft assemblies associated with the requested SEQIDs.

Optional parameters

The supplied documentation does not identify optional parameters for the Redmine ResFinder automator.

Example

2026-SEQ-0001
2026-SEQ-0002

See issue 12854 for an example ResFinder request.

Interpreting results

When ResFinder finishes, it uploads:

resfinder.xlsx

The workbook lists acquired AMR genes detected in each sample. A listed gene or resistance does not by itself establish that the strain expresses the associated resistance phenotype.

Review at least:

  • PercentIdentity — sequence identity between the detected gene and reference target;
  • PercentCovered — coverage of the reference target.

A hit with 100 for both identity and coverage provides stronger evidence that the complete acquired gene is present. Hits with lower identity or coverage require further review.

ResFinder does not report chromosomal point-mutation resistance in this Redmine workflow.

How long does it take?

ResFinder is generally fast and should take only a few seconds per requested SEQID. Total runtime also depends on the number of samples and service workload.

What can go wrong?

A requested SEQID is unavailable

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

Likely cause: ResFinder cannot locate a draft genome assembly for the requested SEQID.

What to do: Verify each SEQID, confirm that its assembly is available, and submit a corrected request.

Point-mutation resistance is missing from the report

Symptom: The ResFinder result does not include an expected chromosomal resistance mutation.

Likely cause: The Redmine ResFinder automator only detects acquired resistance genes.

What to do: Use PointFinder, StarAMR, or CARD-RGI when mutation-based resistance must also be assessed.

A lower-identity or partially covered hit is difficult to interpret

Symptom: A result has less than 100 in PercentIdentity, PercentCovered, or both.

Likely cause: The detected sequence differs from or only partially covers the reference target.

What to do: Review the alignment evidence and organism context before concluding that the complete resistance gene is present.

  • PointFinder — detects supported chromosomal mutations associated with antimicrobial resistance.
  • StarAMR — combines ResFinder acquired-gene detection with PointFinder mutation detection for supported Campylobacter and Salmonella assemblies.
  • CARD-RGI — predicts resistomes in isolate assemblies or raw FASTQ data and can include strict, perfect, loose, and partial CARD hits.
  • GeneSeekr — provides analysis=resfinder for FASTA-formatted inputs.
  • Sipprverse — provides analysis=resfinder for raw, paired-end FASTQ reads.