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Public health genomics resources, kept current.

A cleaner hub for Theiagen documentation, workflow registries, training, protocols, and current SARS-CoV-2 PHB reference materials.

Current TheiaCoV JSONsTraining resources
Public health laboratory staff transfer sealed specimens into a surveillance workflow

Current TheiaCoV PHB reference JSONs

Current public SARS-CoV-2 Terra input JSONs for PHB v2.0.0 or higher. Last updated June 11, 2026.

ClearLabs PHB input JSON

Current TheiaCoV ClearLabs input JSON for PHB v2.0.0 or higher.

  • TheiaCoV_ClearLabs_PHB_2026-06-11.json
Download JSON

FASTA PHB input JSON

Current TheiaCoV FASTA input JSON for PHB v2.0.0 or higher.

  • TheiaCoV_FASTA_PHB_2026-06-11.json
Download JSON

Illumina PE PHB input JSON

Current paired-end Illumina TheiaCoV input JSON for PHB v2.0.0 or higher.

  • TheiaCoV_Illumina_PE_PHB_2026-06-11.json
Download JSON

Illumina SE PHB input JSON

Current single-end Illumina TheiaCoV input JSON for PHB v2.0.0 or higher.

  • TheiaCoV_Illumina_SE_PHB_2026-06-11.json
Download JSON

ONT PHB input JSON

Current Oxford Nanopore TheiaCoV input JSON for PHB v2.0.0 or higher.

  • TheiaCoV_ONT_PHB_2026-06-11.json
Download JSON

Core practitioner resources

Use these paths for documentation, public repositories, workflow registries, protocols, and Terra-oriented training.

Read the Docs

Theiagen public health genomics documentation and workflow guidance.

Open docs

GitHub

Public repositories and open workflow resources from Theiagen.

Open GitHub

Dockstore

Workflow access for Terra and related genomics workflow execution.

Open Dockstore

Protocols.io

Sequencing protocols, including SARS-CoV-2 protocol resources.

Open protocols

YouTube

Public videos and practical training for Theiagen workflows.

Open YouTube

Terra

Cloud workspace access for public health bioinformatics workflows and training contexts.

Open Terra

Implementation notes

These notes keep the page useful without turning it into a long technical archive.

Use the PHB v2.0.0+ section first

Older PHVG and early PHB references are useful for archival context, but the current SARS-CoV-2 recommendations are in the PHB v2.0.0+ group.

Confirm workflow-specific optional inputs

Some optional inputs, including Pangolin Docker image attributes, may move between Terra workflow task locations as workflows evolve.

Use public documentation for current guidance

Reference files, workflow inputs, and recommended settings can change over time, so teams should confirm current guidance before reusing archived materials.

Training and field learning

A practical set of learning materials for teams building public health bioinformatics confidence.

Rabies genomic surveillance one year later

Recording on moving from wet lab workflow to phylogenetic insight in rabies genomic surveillance.

Watch recording

Training and education

Workshops, customized programs, and practical enablement for workflow operation and interpretation.

Explore training

Technical briefs

Workflow, validation, WDL, Nextflow, Terra, and implementation references.

Open briefs

Need help applying these resources?

Tell us which workflow, pathogen, or training need you are trying to solve.

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