Senior Genomics Data Engineer

Join to apply for the Senior Genomics Data Engineer role at Helix
.

Who We Are & What We Do At Helix, our mission is simple: to help everyone improve their lives through their DNA. Ready to make a real-world impact with your skills? At Helix, we're transforming healthcare by making genomics a standard of care. We partner with health systems and life science companies to accelerate the integration of genomic data into clinical practice.

Join us in building a future where healthcare is personalized, proactive, and powered by genomics.

The Helix Clinicogenomic Data Engineering team plays a pivotal role in Helix’s efforts to provide a best-in-class clinico-genomics research dataset for our partners to conduct and publish cutting-edge genomic studies and operational insights back to health systems. Working closely with our Research, Bioinformatics, and Engineering teams, we are responsible for a RUO-genomics dataset as well as developing various programmatic interfaces to facilitate easy access to enable our scientists and analysts.

The patient is top of mind in everything we do, and your contributions here have the opportunity to improve the real world outcomes for everyone.

As a Senior Genomics Data Engineer, you will:

• Leverage your specialized knowledge to develop innovative solutions that simplify complex genomic data, effectively lowering the barrier to entry for non-expert users.
• Design, build, and continuously optimize robust, scalable, and automated data pipelines for processing large-scale genomic and clinical data.
• Build and maintain critical pipelines to prepare, de-identify, and securely deliver massive-scale genetic datasets to both internal research teams and external partners.
• Work cross-functionally with world-class Engineering, Research, AI, Data Science, Bioinformatics, Product, and Commercial teams to tackle complex data challenges and drive scientific discovery.
• Provide expert-level support and create tooling to help internal and external data consumers effectively utilize our complex datasets and platforms.
• Implement and manage data infrastructure as code using tools like AWS CDK, ensuring our distributed compute environment is efficient and scalable.

• Bachelor's/Master's degree in Computer Science, Bioinformatics, Engineering or a related field with 5+ years of experience
• Deep domain knowledge in molecular biology, next-generation sequencing, or genomics
• Demonstrated experience in processing a variety of large scale genetic data formats (exome/whole genome), including but not limited to VCF, CRAM, BAM, and PLINK.
• Strong experience using industry-standard bioinformatics tools such as bcftools, htslib, and samtools.
• Experience with genomic data-reduction techniques, such as PCA
• Expert-level proficiency in Python
• Proven experience designing and building distributed systems on AWS, including expertise with services like Glue, EMR, S3, Lambda, and Dynamo
  
  DB.
• Proficiency with infrastructure-as-code frameworks (e.g., AWS CDK, Terraform).
• Expertise with ETL pipeline automation and workflow management tools such as Airflow, AWS Glue, AWS Step Functions, and CI/CD
• Familiarity with database design, data manipulation, and data quality techniques
• Demonstrated ability to thrive in a fast-paced, adaptable environment.

• Background in the bioinformatics or healthcare industries, and familiarity with clinical data.
• Proficiency in Go, Java, C, C++, or Scala
• Hands‑on skills with genomics‑specific data tools such as Hail or TileDB
• Track records of working in a regulated data environment (e.g., HIPAA)
• Hands‑on experience designing and building distributed systems on AWS, frameworks such as Spark, Dask, EMR, Databricks, or similar

• Recruiter Screen
• Manager Screen/Tech Screen
• Onsite
• Offer

• Base Salary: $145,000 - $201,250
• Annual Bonus: 10% of your annual salary
• Equity:
  We offer generous equity  you receive a Helix offer your recruiter will book dedicated time with you to educate you on our equity model.

• Comprehensive Health Insurance with Date of Hire eligibility (Above average employer paid premium coverage)
• 12…