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_diphtOscan_ is a tool to search genomic assemblies of _Corynebacterium diphtheriae_ and other species of the _Corynebacterium diphtheriae_ species complex (CdSC) for:
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* Species (e.g. _C. diphtheriae_, _C. ulcerans_, _C. pseudotuberculosis_, _C. belfantii_, _C. rouxii_ and _C. silvaticum_)
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* Biovar-associated genes (_spuA_, nitrate reductase gene cluster)
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| ... | ... | @@ -5,4 +7,5 @@ _diphtOscan_ is a tool to search genomic assemblies of _Corynebacterium diphther |
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* Virulence factors, including _tox_ gene detection and disruption prediction
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* Antimicrobial resistance determinants: acquired genes (_ermX_, _pbp2m_, …) and SNPs (e.g., _rpoB_, _gyrA_)
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* Genomic context of genomic features associated with resistance
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* Presence of integrons |
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* Presence of integrons (using Integron Finder: https://github.com/gem-pasteur/Integron_Finder)
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* Tree building (using JolyTree: https://gitlab.pasteur.fr/GIPhy/JolyTree) |
