abriTAMRAntimicrobial gene detection in abriTAMR is based on analyzing assembled genomes from WGS data, where contigs are screened for resistance genes. Genes are considered fully present if >90% of the target protein is identified with >90% identity, while partial matches are reported when 50–90% of the gene is detected. abriTAMR also classifies genes into drug classes using NCBI annotations and in-house assessments, allowing for the detection of alleles with mutations and genes spanning contig boundaries.Versions

v1.3.0 (default)

Tags: bioinformatics, AMR detection, AMRFinderPlus, cpgParameters

contigs (file, multiple) required: Input contigs

species (enum): Specify species to acquire resistance mechanisms as point mutations (optional). Options: Acinetobacter_baumannii, Burkholderia_cepacia, Burkholderia_pseudomallei, Burkholderia_mallei, Campylobacter, Citrobacter_freundii, Clostridioides_difficile, Corynebacterium_diphtheriae and 20 more

Links

Open abriTAMR in the CPG Portal. Configuring and running a tool needs JavaScript.