Cauris_CladeTyper¶
NEEDS WORK!!!!
This page is under construction and will be updated soon.
Quick Facts¶
| Workflow Type | Applicable Kingdom | Last Known Changes | Command-line Compatibility | Workflow Level |
|---|---|---|---|---|
| Standalone | Mycotics | PHB v1.0.0 | Yes | Sample-level |
Cauris_CladeTyper_PHB¶
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.
Inputs¶
Workflow Tasks¶
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 signature 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.