Overview

The TheiaEuk_PE workflow is for the assembly, quality assessment, and characterization of fungal genomes. It is designed to accept Illumina paired-end sequencing data as the primary input. It is currently intended only for haploid fungal genomes like Candida auris. Analyzing diploid genomes using TheiaEuk should be attempted only with expert attention to the resulting genome quality.

All input reads are processed through “core tasks” in each workflow. The core tasks include raw-read quality assessment, read cleaning (quality trimming and adapter removal), de novo assembly, assembly quality assessment, and species taxon identification. For some taxa identified, “taxa-specific sub-workflows” will be automatically activated, undertaking additional taxa-specific characterization steps, including clade-typing and/or antifungal resistance detection.

Overview

Inputs

Core tasks (performed for all taxa)

Taxa-specific tasks

Outputs