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![LogoDiphtOscan](uploads/4d75f18ef982358a4a316a6e884e0ae8/LogoDiphtOscan.png)
_diphtOscan_ is a tool to search genomic assemblies of _Corynebacterium diphtheriae_ and other species of the _Corynebacterium diphtheriae_ species complex (CdSC) for: _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. pseudotuberculosis_, _C. belfantii_, _C. rouxii_ and _C. silvaticum_) * Species (e.g. _C. diphtheriae_, _C. ulcerans_, _C. pseudotuberculosis_, _C. belfantii_, _C. rouxii_ and _C. silvaticum_)
* Biovar-associated genes (_spuA_, nitrate reductase gene cluster) * Biovar-associated genes (_spuA_, nitrate reductase gene cluster)
...@@ -5,4 +7,5 @@ _diphtOscan_ is a tool to search genomic assemblies of _Corynebacterium diphther ...@@ -5,4 +7,5 @@ _diphtOscan_ is a tool to search genomic assemblies of _Corynebacterium diphther
* Virulence factors, including _tox_ gene detection and disruption prediction * Virulence factors, including _tox_ gene detection and disruption prediction
* Antimicrobial resistance determinants: acquired genes (_ermX_, _pbp2m_, …) and SNPs (e.g., _rpoB_, _gyrA_) * Antimicrobial resistance determinants: acquired genes (_ermX_, _pbp2m_, …) and SNPs (e.g., _rpoB_, _gyrA_)
* Genomic context of genomic features associated with resistance * Genomic context of genomic features associated with resistance
* Presence of integrons * Presence of integrons (using Integron Finder: https://github.com/gem-pasteur/Integron_Finder)
* Tree building (using JolyTree: https://gitlab.pasteur.fr/GIPhy/JolyTree)