Bioinformatics Engineer - Production Pipelines (Clinical NGS)
Bioinformatics Engineer - Production Pipelines (Clinical NGS)
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1 Vacancy
Job Description
SAGA Diagnostics is a personalized cancer diagnostics and disease monitoring company focused on molecular genetic analysis of circulating tumor DNA (ctDNA). The companys mission is to improve precision cancer medicine provide more accurate treatment monitoring and improve patient survival using minimally-invasive liquid biopsy cancer testing services. SAGAs 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
Bachelors degree with at least 4 years of relevant industry experience (genomics NGS clinical diagnostics) or Masters 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 SAGAs 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 companys 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 SAGA Diagnostics is a participant in the E-Verify program learn more about the program and review our required disclosures and .
Employment Type
Full-Time
