The TheiaProk workflows are for the assembly, quality assessment, and characterization of bacterial genomes. There are currently four TheiaProk workflows designed to accommodate different kinds of input data:

Illumina paired-end sequencing (TheiaProk_Illumina_PE)
Illumina single-end sequencing (TheiaProk_Illumina_SE)
ONT sequencing (TheiaProk_ONT)
Genome assemblies (TheiaProk_FASTA)

All input reads are processed through “core tasks” in the TheiaProk Illumina and ONT workflows. These undertake read trimming and assembly appropriate to the input data type. TheiaProk workflows subsequently launch default genome characterization modules for quality assessment, species identification, antimicrobial resistance gene detection, sequence typing, and more. For some taxa identified, “taxa-specific sub-workflows” will be automatically activated, undertaking additional taxa-specific characterization steps. When setting up each workflow, users may choose to use “optional tasks” as additions or alternatives to tasks run in the workflow by default.

Page Contents

Workflows available

Overview

Inputs

Core tasks (performed for all taxa)

Taxon-specific tasks

Outputs