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sn_staramr.pl.md

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SYNOPSIS

sn_staramr.pl

Runs antimicrobial resistance analysis

Software requirements

  • StarAMR >= 0.7.0
  • StarAMR database

StarAMR database

Build the database into the correct folder under SneakerNet like so

staramr db build --dir SneakerNet/db/staramr

Under taxonProperties.conf, add the following line under each taxon for pointfinder (SNP) resistance detection. Most taxa are not supported right now. At the time of this documentation, only these are supported: salmonella, campylobacter, enterococcus faecalis and enterococcus faecium.

pointfinder=salmonella

Algorithm

Runs StarAMR on genome assemblies with Pointfinder.

Outputs

Table with columns

  • Sample - sample name
  • Assembly - which assembly was input
  • Genotype
  • Predicted Phenotype