Supporting the genomic infrastructure your community depends on.
Whether you're building a genomic surveillance capability from scratch or running a mature program that needs deeper expertise, Theiagen provides the science, systems, and strategy to get there.
We understand your world
Public health labs are under more pressure than ever — more pathogens, more variants, more demand for faster, and confident outbreak clarity. Some are still building the infrastructure to get there. Others have mature programs but face a different challenge: staff turnover, hard-to-fill bioinformatics roles, NGS pipeline automation that needs to evolve, or complex cases that go beyond what's been seen before.
Wherever you are, the core question is the same: when a specimen comes in, can your lab tell — quickly and accurately — whether it's linked to an outbreak or not?
That’s the question Theiagen was built to answer.
If you're building your program
Your challenges
- Standing up a genomic surveillance program without a clear roadmap or internal bioinformatics expertise
- Building workflows that produce reliable, actionable outbreak intelligence — not just raw sequencing data
- Training staff to own and support the program long term
- Meeting any CDC, federal and state reporting requirements while the program is still being stood up
- Working in Terra and Manifold without the in-house expertise to build and optimize workflows on the platform
How Theiagen helps
We start where you are. Whether you need foundational infrastructure, a specific pathogen surveillance workflow, or both — we build the genomic pipelines and Terra workflows your program needs, train your team on bioinformatics best practices and result interpretation across viral, bacterial, and fungal pathogens, and stay alongside you as your program grows. The result is a lab that can answer the outbreak question independently — repeatedly and reliably.
If your program is already running
Your challenges
- Staff turnover that sets the program back — people leave and capability walks out the door with them
- Funded but understaffed — budget and mandate exist, but bioinformaticians and genomic epidemiologists are hard to find and harder to keep
- New staff who need to be brought up to speed without disrupting operations
- Terra or other platform workflows that need to be built, maintained, or updated as pathogens evolve
- Complex cases — novel pathogens, unusual clusters, AMR patterns your team hasn't encountered before
- Discipline missing talent — strong sequencing capability but limited epidemiological interpretation, or vice versa
- Keeping workflows current as the science and the pathogen landscape move forward
How Theiagen helps
We start with where you are. We identify the gaps — a workflow, a pathogen type, a discipline, or a staffing hole — and build what’s missing without disrupting what is working. We train new staff on existing workflows and bring them up to speed on bioinformatics and result interpretation. And we provide ongoing expert support for complex cases, Terra workflow evolution, and novel pathogens your team hasn’t encountered before. We become the expert bench your lab pulls on — so staff turnover never sets your program back.
Why trust Theiagen
Theiagen brings the full breadth of pathogen expertise — microbiology, bioinformatics, epidemiology, and software systems — to organizations that need reliable, proven genomic intelligence at scale. Our track record across 40+ public health labs demonstrates the scientific depth, operational reliability, and breadth of pathogen coverage our clients depend on.
Frequently Asked Questions
How can Theiagen help public health laboratories with genomic surveillance?
Theiagen helps organizations at every stage of pathogen genomics — from launching a new genomic surveillance program to scaling established public health bioinformatics capabilities and supporting complex investigations. We provide bioinformatics workflows, training, scientific expertise, and ongoing support that transform sequencing data into actionable outbreak intelligence.
How does genomic sequencing help public health laboratories identify outbreaks?
Whole genome sequencing allows laboratories to compare pathogen genomes at the strain level, determining whether cases share the same genetic signature or represent unrelated introductions. This distinction is critical for confirming outbreaks, mapping transmission chains, and directing public health resources where they are needed most.
Can Theiagen train public health laboratory staff on bioinformatics?
Yes. Theiagen provides hands-on training in public health bioinformatics workflows, result interpretation, and best practices for pathogen surveillance across bacterial, viral, and fungal pathogens. Training is tailored to your team’s experience level and designed to build long-term internal capability.
What happens when key bioinformatics staff leave a public health laboratory?
Staff turnover is one of the most common challenges facing genomic surveillance programs. Theiagen provides continuity by training new team members, supporting existing workflows, and filling critical expertise gaps. We become an extension of your team so capability is never dependent on a single individual.
How does Theiagen support Terra workflow development for public health laboratories?
Theiagen builds, optimizes, and maintains Terra workflows for pathogen surveillance and outbreak investigation, including quality control, genome assembly, variant calling, cluster analysis, and interpretation across bacterial, viral, and fungal pathogens.
Can Theiagen support both new and mature genomic surveillance programs?
Yes. We support laboratories at every stage of maturity — from standing up new programs to helping established laboratories optimize workflows, address staffing gaps, and tackle complex investigations.
Does Theiagen use open-source bioinformatics tools for public health workflows?
Yes. Theiagen’s public health genomics workflows are built on open-source bioinformatics tools including Nextflow, WDL, and publicly maintained pipeline frameworks. This ensures transparency, reproducibility, and interoperability across laboratory environments.
How do public health laboratories build sustainable pathogen genomics programs?
Sustainable programs require standardized workflows, workforce development, cross-training, documentation, and ongoing scientific expertise that ensure capability remains resilient despite staffing changes and evolving pathogen threats.
What pathogens can genomic surveillance monitor?
Genomic surveillance can support bacterial, viral, fungal, foodborne, waterborne, and antimicrobial-resistant pathogens. Programs are typically tailored to an organization’s surveillance priorities and emerging threats.
Why is genomic surveillance becoming increasingly important for public health laboratories?
As pathogens evolve, antimicrobial resistance increases, and outbreaks spread more rapidly, public health bioinformatics and genomic surveillance provide the precision needed to detect threats earlier and support timely public health action.