ResFinder

What does it do?

ResFinder is a program developed by the Danish Center for Genomic Epidemiology for detection of antibiotic resistance in draft genome assemblies. It is very important to note that the Redmine version will only look for acquired antibiotic resistance genes (generally plasmid-borne) and not chromosomally encoded AMR genes that are caused by point mutations.

If you're interested in chromosomally encoded AMR genes, use the PointFinder automator or you can External Retrieve your assemblies of interest and submit them to an alternate AMR predictor, such as McMaster's CARD.

How do I use it?

Subject

In the Subject field, put ResFinder. Spelling counts, but case sensitivity doesn't.

Description

All you need to put in the description is a list of SEQIDs you want to detect AMR in, one per line.

Example

For an example ResFinder, see issue 12854.

Interpreting Results

ResFinder will upload a file called resfinder.xlsx once it has completed, which shows every AMR gene found in each sample. Just because a gene/resistance is listed here does not necessarily mean the strain carries that resistance - it's important to look at the PercentIdentity and PercentCovered columns. You can be pretty sure that anything with 100 for both is actually there, but anything else requires further analysis to be sure.

How long does it take?

ResFinder is very fast - it should only take a few seconds to analyze each SEQID requested.

What can go wrong?

1) Requested SEQIDs are not available. If we can't find some of the SEQIDs that you request, you will get a warning message informing you of it.