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phac-nml / staramr

Scans genome contigs against the ResFinder, PlasmidFinder, and PointFinder databases.
Apache License 2.0
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Customize threshold for hit detection #143

Closed andreaniml closed 2 years ago

andreaniml commented 2 years ago

Hi!

Silly question, in abricate I can set the minimal coverage I want for a hit, is it possible to do so in staramr?

Cheers!

apetkau commented 2 years ago

Hello @andreaniml ,

I assume by coverage you mean the overlap between a blast hit and the gene in question? You may want to check out the BLAST Options of staramr (in particular the --percent-length-overlap-* options):

BLAST Thresholds:
  --pid-threshold PID_THRESHOLD
                        The percent identity threshold [98.0].
  --percent-length-overlap-resfinder PLENGTH_THRESHOLD_RESFINDER
                        The percent length overlap for resfinder results [60.0].
  --percent-length-overlap-pointfinder PLENGTH_THRESHOLD_POINTFINDER
                        The percent length overlap for pointfinder results [95.0].
  --percent-length-overlap-plasmidfinder PLENGTH_THRESHOLD_PLASMIDFINDER
                        The percent length overlap for resfinder results [60.0].
andreaniml commented 2 years ago

Yes! That was exactly what I was looking for, thanks!