AMR detection workflows
WF1 ISO abritAMR
Multi SpeciesDoi: 10.1038/s41467-022-35713-4
abriTAMR is an AMR gene detection pipeline that runs AMRFinderPlus on a single (or list ) of given isolates and collates the results into a table, separating genes identified into functionally relevant groups. abriTAMR is accredited by NATA for use in reporting the presence of reportable AMR genes in Victoria Australia. Acquired resistance mechanims in the form of point mutations (restricted to subset of species) Streamlined output. Presence of virulence factorsView on WorkflowHub
Escherichia coliDoi: 10.1099/mgen.0.000531
With this galaxy pipeline you can use Escherichia coli next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard E. coli phenotypic isolates.
This pipeline is based on the work of Sciensano, Belgium.
Salmonella speciesDoi: 10.3389/fmicb.2020.00549
With this galaxy pipeline you can use Salmonella sp. next generation sequencing results to predict bacterial AMR phenotypes and compare the results against gold standard Salmonella sp. phenotypes obtained from food.
This pipeline is based on the work of the National Food Agency of Canada.