Bioinformatics Engineer - Production Pipelines (Clinical NGS)

SAGA Diagnostics is a personalized cancer diagnostics and disease monitoring company focused on molecular genetic analysis of circulating tumor DNA (ctDNA). The company’s mission is to improve precision cancer medicine, provide more accurate treatment monitoring, and improve patient survival using minimally-invasive liquid biopsy cancer testing services. SAGA’s proprietary tests can help patients, oncologists, and drug developers detect actionable mutations, stratify patient groups, and monitor treatment response, residual disease, and disease recurrence at unprecedented sensitivity and scale.

We are seeking a Bioinformatics Engineer with a strong technical background and a deep expertise in developing and maintaining production-grade pipelines for clinical next generation sequencing data (NGS). The role is ideal for someone who thrives at the intersection of software engineering and genomics, and who brings rigor to implementing, testing and continuous improvement of computational systems in a regulated environment.

Responsibilities:

• Develop, implement and maintain robust, scalable pipelines for the analysis of Illumina whole genome sequencing data, with an emphasis on structural variant calling and QC metrics.
• Apply software engineering best practices including modular code development, unit testing, code reviews, documentation, and continuous integration to ensure reproducibility, maintainability, and compliance.
• Collaborate with cross-functional teams (R&D, QA, software, clinical operations) to identify opportunities to drive improvements in pipeline design, execution, automation and streamline data processing and analysis.

• Troubleshoot pipeline failures and bugs across production environments, conduct in-depth root cause analyses, and implement fixes with appropriate validation strategies and documentation, in accordance with quality standards.
• Optimize cloud infrastructure (primarily AWS) for performance, reliability, and cost-efficiency in high-throughput data processing.
• Optimize cloud infrastructure for cost-effective and scalable NGS data processes, primarily on AWS.

Requirements

• MSc (with 5+ years industry experience) or PhD (with 3+ years industry experience) in bioinformatics, computer science, computational biology, or a related field. Prior experience in a clinical genomics or molecular diagnostics setting highly preferred.
• Strong programming skills in Python and proficiency in Linux/Bash.
• Demonstrated application of software development best practices, including version control (Git), CI/CD pipelines (GitHub Actions, GitLab CI, etc.), testing frameworks, and issue tracking systems.
• Experience in developing and deploying production bioinformatics workflows using workflow languages such as Nextflow or Snakemake.
• Experience with containerization technologies such as Docker or Singularity, and environment management with Conda or similar tools.
• Hands-on experience with cloud-based infrastructure (preferably AWS) for scalable data analysis workflows.
• Familiarity with software QA processes, including verification and validation (V&V) in clinical or regulated environments.
• Excellent written and verbal communication skills in English.

Preferred qualifications:

• Experience with Illumina sequencing data, including alignment, variant calling (especially SVs) and read-level QC.
• Strong grasp of cancer biology and molecular diagnostics.
• Experience with relational databases (SQL).
• Exposure to statistical or machine learning approaches for genomics data analysis.

What we offer:

• The opportunity to work with an incredible team with access to fantastic data
• As a member of a small team, you will be involved in every aspect of the business and help set the direction/culture as we grow.
• You will be given the autonomy and resources to deliver to the highest level.
• All the perks of a start-up – membership to SAGA’s Equity plan, highly competitive salaries, exciting technology and innovation, and a dynamic work environment.

Benefits

• Competitive Compensation and company wide benefits plan 

• Opportunities for career advancement and professional development.

• A collaborative and innovative work environment dedicated to improving oncology outcomes.

SAGA Diagnostics is an equal opportunity employer, fully committed to achieving a diverse and inclusive workplace that embraces and encourages applicants of every background.  The company’s policy regarding equal employment opportunity means that all decisions regarding recruitment, hiring, benefits, wage and salary administration, scheduling, disciplinary action and termination will be made without unlawful discrimination on the basis of sex, gender, race, color, age, national origin, religion, disability, medical condition, genetic information, marital status, sexual orientation, gender identity or expression, citizenship status, pregnancy or maternity, veteran status, or any other status protected by applicable federal, state or local law. If you require reasonable accommodation in completing an application, interviewing, or otherwise participating in the employee selection process, please direct your inquiries to hr@sagadiagnostics.com. SAGA Diagnostics is a participant in the E-Verify program, learn more about the program and review our required disclosures  and .