diphtOscan is a tool to search genomic assemblies of Corynebacterium diphtheriae and other species of the Corynebacterium diphtheriae species complex (CdSC) for:
- Species (e.g. C. diphtheriae, C. ulcerans, C. ramonii, C. pseudotuberculosis, C. belfantii, C. rouxii and C. silvaticum)
- Biovar-associated genes (spuA, nitrate reductase gene cluster)
- MLST sequence type
- Virulence factors, including tox gene detection and disruption prediction
- Antimicrobial resistance determinants: acquired genes (ermX, pbp2m, …) and SNPs (e.g., rpoB, gyrA)
- Genomic context of genomic features associated with resistance
- Presence of integrons (using Integron Finder: https://github.com/gem-pasteur/Integron_Finder)
- Tree building (using JolyTree: https://gitlab.pasteur.fr/GIPhy/JolyTree)