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Freyja Wastewater Analysis Series
The Cauris_CladeTyper_PHB Workflow is designed to assign clade to Candida auris Whole Genome Sequencing assemblies based on their genomic sequence similarity to the five clade-specific reference files. Clade typing is essential for understanding the epidemiology and evolutionary dynamics of this emerging multidrug-resistant fungal pathogen.
The Cauris_Cladetyper Workflow for Candida auris employs GAMBIT for taxonomic identification, comparing whole genome sequencing data against reference databases to accurately classify Candida auris isolates. A custom database featuring five clade-specific Candida auris reference genomes facilitates clade typing. Sequences undergo genomic signiture comparison against the custom database, enabling assignment to one of the five Candida auris clades (Clade I to Clade V) based on sequence similarity and phylogenetic relationships. This integrated approach ensures precise clade assignments, crucial for understanding the genetic diversity and epidemiology of Candida auris.
The output of this workflow is the Candida auris clade assignment.
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