StarAMR
What does it do?
StarAMR is a program from Canada's National Microbiology Laboratory that combines the ResFinder and PointFinder programs for detecting antibiotic resistance from the Danish Center for Genomic Epidemiology.
How do I use it?
Subject
In the Subject field, put staramr. 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. Note that StarAMR is limited to detecting mutations in a few genera:
- Campylobacter
- Salmonella
Our StarAMR automator will automatically determine the genus of your requested SEQIDs, and will not attempt to analyze any SEQIDs that are not from one of these genera.
Example
For an example StarAMR, see issue 15625.
Interpreting Results
StarAMR will upload a zip file called staramr_output.zip. Within this folder, you will find a few files for each genus:
Note: Any SEQIDs from genera that are not Campylobacter or Salmonella not have any files uploaded
The most important file for each genus is results.xlsx - this shows what AMR genes were found in each
SeqID, and also lets you see if the resistance is conferred by a gene or a point mutation.
How long does it take?
StarAMR should take 30 seconds to 1 minutes for analysis of each sample.
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.
2) Can't run on requested genera: If the SEQIDs you request are not one of the genera that PointFinder works on, you will get a message saying so. PointFinder will still run on any SEQIDs specified that are from the correct genera.