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.

SAGA Diagnostics AB is seeking a highly skilled and experienced Bioinformatics Engineer/Scientist with a strong technical background and a passion for driving innovation in cancer diagnostics.  As a key member of our diverse multi-disciplinary R&D team, you will play a pivotal role in the development, optimization, and enhancement of robust bioinformatics pipelines for our clinical diagnostics platform. We are looking for individuals who excel in improving pipeline efficiency, scalability, and performance in a regulated environment to accelerate downstream data processing, analysis, and interpretation.

This role is ideal for someone who thrives at the intersection of data engineering and biology, and who is motivated by advancing scientific discovery with real-world impact on patient lives.

Responsibilities:

·       Develop, maintain and optimize pipelines for the analysis of Illumina whole genome sequencing data, with a strong emphasis on structural variant calling and quality control metrics.

·       Support production troubleshooting by identifying and resolving issues in data processing pipelines and associated compute environments.

·       Collaborate with cross-functional teams (R&D, QA, software, clinical operations) to identify opportunities for workflow enhancements and drive implementation of innovative solutions to streamline data processing and analysis.

·       Perform in-depth data analysis and root cause analyses of pipeline or data issues and provide insights to guide pipeline improvements and optimize associated workflow processes.

·       Optimize cloud infrastructure for cost-effective and scalable NGS data processes, primarily on AWS.

Requirements

·       Bachelor’s degree with at least 4 years of relevant industry experience (genomics, NGS, clinical diagnostics), or Master’s in bioinformatics, computational biology, computer science or a related field highly preferred.

·       Extensive hands-on experience with Linux/Bash and proficiency in Python.

·       Proven track record of developing, optimizing, and maintaining complex bioinformatics pipelines, utilizing workflow systems like Nextflow or Snakemake, and leveraging tools such as Conda, Docker, or Singularity.

·       Proficiency in version control systems, such as Git, and DevOps software, including GitHub/GitLab, with knowledge of continuous integration and deployment (CI/CD) practices.

·       Familiarity with configuring public cloud providers like Amazon AWS or Microsoft Azure to optimize and scale-up data processing pipelines.

·       Excellent written and verbal communication skills in English.

Preferred qualifications:

·       Previous experience in analyzing Illumina sequencing data, including read alignment and structural variant detection.

·       Strong understanding of (cancer) biology and fundamental genomics concepts.

·       Proficiency in SQL and experience in working with Business Intelligence software, such as Microsoft Power BI or Tableau.

·       Theoretical knowledge and practical experience in machine learning techniques

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 opportuni