Results not matching CGE ResFinder web-interface output about staramr HOT 2 CLOSED

Thanks for reporting the issue @eam12 😄

You are correct, there is a difference in how the CGE web server is choosing the gene to report, and the way staramr is choosing the gene. There are a lot of very similar genes in the ResFinder database, and the logic I implemented tries to choose the "best" result based on the percent identity and gene length. staramr prefers to report longer genes so long as they don't drop the percent identity too much. I am not quite sure what is the "best" gene to pick in these cases where we have very close matches, but this is the logic staramr is currently using. You can take a look at it here https://github.com/phac-nml/staramr/blob/master/staramr/blast/results/BlastResultsParser.py#L110 if you're curious.

staramr does support the option to include all genes in your results if you wanted to do more in-depth inspections. You can run with --report-all-blast in this case. I'm sure if you use this flag you'll see the gene the CGE webserver picked among the list of possible options.

Let me know if you want any more information.

from staramr.

This was very helpful. Thank you very much!

from staramr.