Senior DevOps Engineer for Bioinformatics Pipelines

Position: DevOps Engineer

Position Type: Full-Time Employee

Department: R&D

Location: Boulder, onsite

Experience: BS/MS degree and 4+ years’ industry experience

Watchmaker Genomics is an early-stage life science company based in Boulder, Colorado. Our team is passionate about innovation and values collaboration, creativity and scientific rigor. We believe the intersection of biology, engineering and computer science presents exciting opportunities for developing novel technologies that promote research and improve human health. Watchmaker Genomics specializes in the design, development and production of DNA- and RNA-modifying enzymes that enable high-growth applications in genomics, molecular diagnostics and personalized medicine.

Watchmaker is inviting applications for the full-time position of DevOps Engineer.

This role reports to the Bioinformatics Engineering Team Lead and focuses on developing the cloud infrastructure and platform services that power scalable bioinformatics pipelines and self-service analytics. This individual will lead projects involving the design, development, and implementation of reusable software services and infrastructure templates to enable research scientists, product developers, and other stakeholders to extract information critical to the development of innovative enzyme-based products for the growing genomics space. The development of automated analytical pipelines requires rigorous, scalable software development and testing, ideally involving a working understanding of existing tools for sequence data analysis. The ideal candidate will have a firm understanding of cloud-native development methodologies (CI/CD, IAC, observability, monitoring, debugging) and software engineering principles. The candidate will be exposed to cutting edge molecular biology and genomics technologies.

The successful candidate will thrive in a dynamic, fast-paced working environment, be an excellent communicator, and contribute directly to our company culture and success.

Responsibilities

• Maintain and extend self-service bioinformatics software platforms and infrastructure
• Ensure platform reliability, scalability, and maintainability by proactively identifying weak points, improving resilience, and reducing manual intervention
• Own Terraform codebase and CI/CD pipelines to enable reproducible multi-environment deployments (production, staging, test, developer) across AWS accounts
• Develop containerized build environments (e.g., Docker) and automation services (e.g., Lambdas, event-driven APIs) to standardize workflows and integrate systems
• Contribute to efficient data management strategies, including standardized ingestion and preprocessing of NGS datasets
• Collaborate with R&D teams to build infrastructure and services that accelerate scientific discovery

Skills and Requirements

The candidate should have a BS/MS degree with 4+ years’ experience, or equivalent years of industry background. Experience in biotech and a start-up environment are highly desirable.

The candidate must have a proven track record of developing scalable, observable, and robust software systems and cloud infrastructure. Strong software development skills and expertise with DevOps tools and concepts are required. Experience with / exposure to other areas including structural biology, bioinformatics algorithms, and next-generation sequencing platforms are a plus.

The following skills and experience are requirements for the position:

• 4+ years in a mixed Software Engineering and DevOps/Infrastructure role, or comparable related experience, ideally in a bioinformatics or computational biology setting
• Proficient with AWS tools and infrastructure (e.g. EC2, S3, IAM, ECS, Lambda, Batch, CloudWatch, SQS/SNS)
• Proficient with IAC tools (Terraform preferred), including modular multi-environment design
• Proficiency with at least one programming language (Python preferred)
• Proficiency with containerization tools (e.g. Docker, Apptainer)
• Proficient with CI/CD tools (e.g. Jenkins, Github Actions, GitLab)
• Strong Linux and Bash skills
• Familiarity with workflow orchestration tools (e.g., Nextflow, Snakemake, Airflow) is a plus, but not required
• Proficient with container orchestration systems in a cloud environment
• Experience with observability/monitoring/alerting stacks (e.g., CloudWatch, Datadog, OpenTelemetry)
• Familiarity with data warehousing solutions (e.g. RedShift, Snowflake)
• Excellent interpersonal skills and communication with peers and all levels of management
• Familiar with Scrum and Agile development methodologies
• Excellent organizational skills and attention to detail
• Ability to prioritize, deliver consistently under deadlines, and work independently with initiative
• Good communication and personal task management skills and a high level of self-motivation and initiative
• A creative and disciplined approach to problem-solving

Education and Experience

BS/MS in computer science, information systems, or related degree and a minimum of 4+ years of relevant industry experience, or an equivalent combination of education and experience.

Compensation

The base compensation for the DevOps Engineer role starts at $90,000-$110,000 + bonus + equity; actual pay will be adjusted based on skills and experience. Employees are eligible for Flexible Time Off, Holidays, employer covers 75% of base medical plan with buy-up options, EAP (employee assistance program), employer paid dental, employer paid vision, employer paid $25,000 life/AD&D policy, paid parental leave, and a 401(k) retirement plan with a 4% match.

Application Requirements

To apply for the position, please submit the following in a PDF format on watchmakergenomics.com:

• Letter of motivation (upload where it says cover letter)
• Resume or Curriculum vitae, highlighting relevant qualifications and experience

Applications without a Letter of Motivation will not be considered. Candidates local to the Denver/Metro area preferred.

Applications will be accepted on a rolling basis and the position will remain open until filled; however, early submission is encouraged as review will begin immediately.

If selected to participate in the interview process, the names and contact information of three professional references who are able to assess your suitability for the position in terms of the specified requirements will be requested.

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NO RECRUITMENT AGENCIES PLEASE

We are only accepting direct applications for this position. We are not working with external recruiters or agencies at this time. Unsolicited resumes or candidate submissions from third-party recruiters will not be considered and will be deemed the property of Watchmaker Genomics.

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WE ARE AN EQUAL OPPORTUNITY/AFFIRMATIVE ACTION EMPLOYER

Watchmaker Genomics is committed to being an equal opportunity employer and creating a culturally diverse environment. All qualified applicants will receive consideration for employment without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, disability status, age, or veteran status or any other characteristics as protected by applicable law.

All applicants will be asked if currently eligible to work in the United States of America; and if now or in the future will require visa sponsorship to continue working in the United States.

This position may be subject to pre-employment checks, including driving history check, drug screening and a background check for any convictions directly related to its duties and responsibilities. All pre-employment checks will comply with all applicable federal, state, and local laws.