The Translational Medicine Genomics team is expanding to support cutting-edge Oncology initiatives in big data generation, including DNA sequencing, single-cell, and bulk expression.

We are seeking a skilled and motivated Bioinformatics Pipeline Analyst to take the lead in benchmarking, optimizing, and operating DRAGEN-based somatic tumor/normal analysis workflows. You will ensure robust performance of DRAGEN pipelines across whole exome (WES) and whole genome sequencing (WGS) datasets — driving improvements in accuracy, reliability, and scalability for oncology applications.

Feel free to work remotely from anywhere across Latvia or connect with colleagues at our Riga office.

Responsibilities

• Benchmark and optimize pipeline performance (sensitivity, specificity, runtime, duplicate handling, UMI handling, downsampling)
• Evaluate WES/WGS outputs against reference datasets; generate performance metrics, reports, and recommendations
• Manage and execute DRAGEN tumor/normal pipelines, handling raw sequencing data (FASTQ, BAM, CRAM), configuration, and troubleshooting
• Generate and maintain custom resource files (e.g., reference genomes, annotation databases, systematic noise files)
• Draft comprehensive technical documentation, reports, and best practices; present findings to interdisciplinary teams
• Review Illumina DRAGEN outputs, provide feedback, and recommend improvements

Requirements

• PhD in Bioinformatics, Computational Biology, Data Science, Computer Science, or a related field, with 3+ years of industry experience, OR a Master’s degree with 5+ years of relevant experience
• Proven expertise in human genomics, WGS/WES data analysis, and tumor/normal workflows
• Hands-on experience with Illumina NGS data and DRAGEN pipelines
• Proficiency in Python, R, or similar languages for analysis and automation
• Experience working with cloud environments (AWS preferred)
• Strong track record in pipeline automation, scalability, and reproducibility
• Excellent communication skills and ability to create clear, instructive documentation

Nice to have

• Direct experience with Illumina DRAGEN platform
• Familiarity with CNV, SV, TMB, MSI, and annotation workflows
• Experience with Nextflow or similar pipeline orchestrators
• Hands-on with Domino Data Lab, Jira, and Confluence
• Background in molecular biology, cancer genomics, or related disciplines

We offer

• Engineering Heritage: Best-in-class experts sharing a culture of engineering excellence and tackling complex engineering challenges for over 30 years.
• Advanced Tech Stack: Innovative projects where you can apply or enhance your expertise in Cloud, Data, AI, and other emerging technologies.
• World-Class Clients: Work closely with 295+ of the Forbes Global 2000 on creating disruptive solutions that make a global impact.
• Professional Growth: Exceptional support for career development with comprehensive resources for upskilling or reskilling in pioneering practices.
• GenAI Community: Strong AI competencies with 600+ experts across 55+ locations driving GenAI-enabled transformation journeys.
• Entrepreneurial Culture: If you're passionate and dedicated to improving business transformation, we provide the support you need to bring your ideas to life.
• Hybrid Setup: The flexibility to work from any location in Latvia, whether it's your home or our office in Riga.
• Other Benefits: Additional vacation and trust days, private health insurance, Employee Stock Purchase Plan and more.

About EPAM

EPAM is a leading global provider of digital platform engineering and development services. For over 30 years, our team has helped leading brands navigate the waves of digital transformation, building solutions that help them stay competitive through constant market disruption.With offices in 55+ countries, EPAM has grown in Latvia to over 150+ talented innovators in 3 years. We foster creativity and unconventional ways of doing things, welcoming like-minded professionals to join us.

Salary range €3.5K-€5K gross, based on your experience and interview results.