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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.

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.

Inputs

Core tasks (performed for all taxa)

Taxa-specific tasks

Outputs

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