AWS Bioinformatics Engineer (Full time remote US/Canada)

About you: You have 2-5 years’ experience in high-volume production bioinformatics workflows for WGS and WTS analysis. You've worked in a regulated clinical lab environment and have built tools that help scientists and genetic counselors evaluate data from complex workflows. You excel at taking proof‑of‑concept tools developed by scientists and integrating them into robust, scalable production workflows. You understand the balance between innovation and reliability in a clinical setting.

About the role: This is a hands‑on, high‑agency role where you'll work with our lead bioinformatics engineer to learn the existing pipelines and codebases for data generation. As you gain familiarity with our pipeline and product(s), you will work on new product deployment and suggest improvements to the existing workflows, helping to balance trade‑offs between pipeline speed and costs for stakeholders across the organization. You will share running and monitoring operations duties with existing staff. You'll initially report to our lead bioinformatics engineer and work closely with everyone—founders, clinicians, scientists, and engineers—to keep things aligned, moving, and documented. We're a remote team with quarterly off‑sites and other travel opportunities.

About us: Juniper Genomics is a venture‑backed start‑up using genomics and modern data science to improve IVF success rates and access, reducing the burden of trying to conceive. We recently launched our first product: a whole‑genome preimplantation genetic test (PGT). We are a team of experts in genomics, medicine, ethics and business; and we’re committed to rigorous science paired with thoughtful ethics, kindness, honesty, and respect for families’ informed decisions.

Culture: You will find us to be supportive, flexible, vulnerable, passionate and consensus‑oriented. No Rules Rules, 5 Dysfunctions, Turn the Ship Around, Radical Candor.

Diversity doesn’t come from checklists - if you are excited about this opportunity and even a few of the details below match up, contact us anyway.

What you’ll do:

• Become the primary owner of existing cross‑functional production pipelines, managing software dependencies across operations, clinical, and product teams to ensure timelines and deliverables stay on track.
• Help build and maintain comprehensive documentation for workflows and SOPs as requirements evolve, ensuring processes are scalable, intuitive, and well‑documented.
• Collaborate with internal and external teams to document software releases, updates, and validation processes in accordance with regulatory requirements.
• Monitor and optimize pipeline performance, help identify bottlenecks and implement improvements to enhance throughput, reduce costs, and maintain accuracy.
• Participate in on‑call rotation to ensure continuous operation of critical production systems.

Qualifications:

• 2-5 years of experience building systems in a genomics, healthcare, or research environment, with strong ability to communicate across domains.
• 2+ years of experience in either a clinical or high‑production bioinformatics environment.

Technical Skills:

• Python Engineering : Strong proficiency in Python for production systems, including object‑oriented design, type hints, testing frameworks, and best practices for maintainable production code. Experience with automation and web development frameworks.
• AWS Infrastructure : Extensive hands‑on experience with AWS services including CloudFormation or Terraform for infrastructure as code; S3 for data storage and lifecycle management; EC2 and Batch for compute orchestration; IAM, VPC, and security best practices.
• Nextflow Workflows : Experience building and maintaining Nextflow pipelines, specifically deployed on AWS Batch. Process optimization and resource management.
• Docker : Experience with Docker and containerization strategies.
• GitHub & DevOps : Proficient with GitHub for ticketing, code review, documentation, releases, and CI/CD automation using GitHub Actions.
• Bioinformatics Tools : Familiarity with standard genomics tools and file formats (FASTQ, BAM, VCF, etc.) and variant calling pipelines.
• Definitely helpful if you have experience: working in a biology wet‑lab; working in a CLIA/CAP environment; monitoring CloudWatch observability tools; and/or working in startups, especially with remote teams.

How to apply:

Please send your resume and cover email to jobs@junipergenomics.com. In your cover email, we'd love to hear about a challenging production pipeline you've built or maintained, and how you balanced the competing demands of speed, accuracy, and cost.

Individuals seeking employment at Juniper Genomics are considered without regards to race, color, religion, national origin, age, sex, marital status, ancestry, physical or mental disability, veteran status, gender identity, or sexual orientation, or any other characteristic protected by applicable law.

Juniper Genomics does not accept unsolicited applicants submitted by third‑party recruiters or agencies. Any resume or application submitted to Juniper without a prior agreement in place will be considered unsolicited and property of Juniper, and Juniper will not pay a placement fee.

Seniority level

Mid‑Senior level

Employment type

Full‑time

Job function

Research, Analyst, and Information Technology