AWS Bioinformatics Engineer; remote US​/Canada

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.

• 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.

• 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.

• 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 Cloud Formation 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.
• Git Hub & Dev Ops :
  Proficient with Git Hub for ticketing, code review, documentation, releases, and CI/CD automation using Git Hub Actions.
• Bioinformatics Tools :
  Familiarity with standard genomics tools and file formats (FASTQ, BAM, VCF, etc.) and variant calling…