Watchmaker Genomics is a 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 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.

Position Summary

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

This position reports to the Vice President of Software and Computational Biology and will be responsible for both robust internal pipeline development and cloud infrastructure development in support of our self-service analytical platforms. This individual will lead projects involving the design, development, and implementation of reusable software and cloud infrastructure 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, as well as a working understanding of existing tools for sequence data analysis. The ideal candidate will have a firm understanding of software engineering principles, cloud development methodologies (including CI/CD and IAC concepts), and ideally a basic knowledge of molecular biology and sequencing library preparation.

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.

  • Maintain and extend existing self-service bioinformatics software platforms and infrastructure
  • Ensure that software and infrastructure supporting Watchmaker’s genomics platform is highly available, scalable, and maintainable
  • Develop reusable and repeatable infrastructure deployments using CI/CD platforms (e.g. Jenkins, Github Actions, GitLab) and IAC tools (e.g. Terraform)
  • Monitor metrics and develop ways to improve observability through telemetry gathering, reporting, and alerts
  • Contribute to a highly innovative and efficient R&D computational biology codebase
  • Contribute strategies for efficient data management for the purpose of maximizing learning from new and historical datasets
  • Participate in customer collaborations and product support
  • Identify opportunities for internal process improvement
  • Collaborate with the broader R&D team to understand and implement additional systems and services
Required Qualifications and Experience

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

The following skills and experience are requirements for the position:

  • 4+ years in an mixed Software and DevOps role, or comparable related experience, preferably in a bioinformatics or computational biology setting
  • Proficiency with at least one programming language (Python preferred)
  • Proficiency with Nextflow (preferred) or other workflow tools like Snakemake or Airflow.
  • Strong Linux and Bash skills
  • Proficient with AWS tools and infrastructure (e.g. EC2, S3, IAM, ECS, Lambda, Batch, and CloudWatch),
  • Proficient with CI/CD tools (e.g. Jenkins, Github Actions, GitLab)
  • Proficient with IAC tools (Terraform preferred)
  • Proficient with container orchestration systems in a cloud environment
  • Familiar with Scrum and Agile development methodologies
  • Excellent interpersonal skills and communication with peers and all levels of management
  • Excellent organizational skills and attention to detail
  • The ability to multitask, be able to work at a high standard, perform consistently under pressure along with pre-determined deadlines and work without supervision
  • 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 Requirements

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.


The base compensation for the Software and Infrastructure Developer role starts at $110,000-130,000 + bonus + equity; actual pay will be adjusted based on skills and experience. Employees are eligible for Flexible Time Off, Holidays, Medical, Dental, Vision, Life/AD&D, Short Term Disability, EAP, and a 401(k) retirement plan.

Application Requirements

To apply for the position, please submit the following in a PDF format on

  • Letter of motivation
  • Resume or Curriculum vitae, highlighting relevant qualifications and experience

Applications without a Letter of Motivation will not be considered. Local candidates preferred.

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.



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.