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PHBG workflows
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The TheiaProk workflows are for the assembly, quality assessment, and characterization of bacterial genomes.
There are currently two TheiaProk workflows: one for Illumina paired-end sequencing (TheiaProk_Illumina_PE), and another for Illumina single-end sequencing (TheiaProk_Illumina_SE). Besides the data input types, there are minimal differences between these two workflows.
All input reads are processed through “core tasks” in each workflow. These undertake read trimming and assembly, quality assessment, species identification, and some genome characterization. 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.
versioning: Version Capture for TheiaProkscreen: Total Raw Read Quantification and Genome Size Estimationread_QC_trim: Read Quality Trimming, Adapter Removal, Quantification, and IdentificationCG-Pipeline: Assessment of Read Quality, and Estimation of Genome Coverageshovill: De novo AssemblyQUAST: Assembly Quality AssessmentBUSCO: Assembly Quality AssessmentMUMmer_ANI: Average Nucleotide Identity (optional)GAMBIT: Taxon AssignmentAMRFinderPlus: AMR Genotyping (default)ResFinder: AMR Genotyping (alternative)TS_MLST: MLST ProfilingProkka: Assembly Annotation (default)Bakta: Assembly Annotation (alternative)PlasmidFinder: Plasmid IdentificationQC_check: Check QC Metrics Against User-Defined Thresholds (optional)The TheiaProk workflow automatically activates taxa-specific sub-workflows after identifying relevant taxa using GAMBIT. Such sub-workflows are available for the following taxa:
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