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

Illumina paired-end sequencing (TheiaCoV_Illumina_PE)
Illumina single-end sequencing (TheiaCoV_Illumina_SE)
ONT sequencing (TheiaCoV_ONT)
Genome assemblies (TheiaCoV_FASTA)
ClearLabs sequencing (TheiaCoV_ClearLabs)

Additionally, the TheiaCoV_FASTA_Batch workflow is available to process several hundred SARS-CoV-2 assemblies at the same time.

These workflows currently support the following organisms:

SARS-CoV-2 ("**sars-cov-2**" or "SARS-CoV-2") - default organism input
Monkeypox virus ("**MPXV**" or "mpox" or "monkeypox" or "Monkeypox virus" or "Mpox")
Human Immunodeficiency Virus ("HIV")
West Nile Virus ("**WNV**" or "wnv" or "West Nile virus")
Influenza ("**flu**" or "influenza" or "Flu" or "Influenza")
RSV-A ("**rsv_a**" or "rsv-a" or "RSV-A" or "RSV_A")
RSV-B ("**rsv_b**" or “rsv-b” or "RSV-B" or "RSV_B")

The compatibility of each workflow with each pathogen is shown below.

	SARS-CoV-2	MPXV	HIV	WNV	Influenza	RSV-A	RSV-B
Illumina_PE	✅	✅	✅	✅	✅	✅	✅
Illumina_SE	✅	✅	❌	✅	❌	✅	✅
ClearLabs	✅	❌	❌	❌	❌	❌	❌
ONT	✅	✅	✅	❌	✅	✅	✅
FASTA	✅	✅	❌	✅	✅	✅	✅

We’ve provided the following information to help you set up the workflow for each organism in the form of input JSONs.

<aside> 🗝️ Key resources

Docker Image and Reference Materials for SARS-CoV-2 Genomic Characterization

Workspace Reference Materials for MPXV Genomic Characterization

HIV
WNV
Flu
RSV-A
RSV-B </aside>

All input reads are processed through “core tasks” in the TheiaCoV Illumina, ONT, and ClearLabs workflows. These undertake read trimming and assembly appropriate to the input data type. TheiaCoV workflows subsequently launch default genome characterization modules for quality assessment, and additional taxa-specific characterization steps. When setting up the workflow, users may choose to use “optional tasks” as additions or alternatives to tasks run in the workflow by default.

Workflows available

Overview

Inputs

Organism-specific parameters and logic

Core tasks

Assembly tasks

Organism-specific characterization tasks

Outputs