Software Developer; Genomics Analysis Team

Berkeley Lab's (LBNL) Joint Genome Institute (JGI) has an opening for a Software Developer to join the Genomics Analysis Team!

In this exciting role, you will support the development, maintenance, and optimization of critical infrastructure that supports large‑scale genomics research. The position focuses on automating a diverse set of genome‑analysis pipelines and their quality‑control processes, enabling the Institute to process tens to hundreds of thousands of samples for large‑scale scientific initiatives.

This hands‑on role involves building and maintaining next‑generation sequencing (NGS) data‑processing pipelines, working with relational databases for genomics data, and creating internal web applications for data visualization and pipeline monitoring. You will work with a substantial existing codebase, learning complex systems while adding new functionality based on scientific and operational requirements. Day‑to‑day responsibilities include troubleshooting production systems, supporting ad‑hoc analyses for research staff, designing and developing new systems, and producing clear, high‑quality technical documentation.

The Joint Genome Institute (JGI) is a global leader in genome science, helping shape the future of biological discovery through advanced genomic capabilities, expert support, and large‑scale, AI‑ready data resources. As a DOE Office of Science user facility, JGI advances a mission to achieve a predictive understanding of complex biological, Earth, and environmental systems in support of national infrastructure security. The institute is headquartered in Berkeley, CA.

This position has an anticipated start date of July 1, 2026.

• Troubleshoot complex systems and monitor performance across production data pipelines.
• Develop and maintain pipelines for processing next‑generation sequencing (NGS) data.
• Design and maintain relational databases supporting large‑scale genomics data.
• Build and maintain internal web applications for system monitoring and data visualization.
• Maintain and enhance a substantial codebase distributed across several code repositories.
• Implement new functionality based on evolving scientific and operational requirements.
• Produce high‑quality documentation for software systems and analytical approaches.
• Provide technical support for ad‑hoc genomics analysis in collaboration with scientific staff.

• A minimum of 5 years of professional experience as a Software Engineer.
• Experience developing and integrating RESTful web services and creating web applications using HTML, CSS, and JavaScript.
• Demonstrated proficiency with querying and designing schemas for relational databases.
• Hands‑on experience using Git and collaborative version‑control workflows.
• Proficiency with BASH scripting, Python, and commonly used libraries such as pandas, matplotlib, Pillow, and FastAPI.
• Demonstrated track record of maintaining, enhancing, and supporting complex codebases.
• Ability to manage multiple projects and competing priorities effectively in a fast‑paced environment.
• Strong analytical and problem‑solving skills, including the ability to identify problems, troubleshoot effectively, and exercise sound judgment in selecting methods and techniques for obtaining solutions.
• Excellent oral and written communication skills, including experience organizing and presenting technical information to varying audiences.
• Demonstrated interpersonal and collaboration skills, including experience working effectively within an interdisciplinary research team.

• A Bachelor's Degree (or equivalent knowledge/training) in Computer Science or a related field.
• Experience with CI/CD pipelines and automated testing.
• Experience with Linux system administration and containerization technologies (Docker, Singularity).
• Experience with HPC computing environments and job schedulers (SLURM).
• Hands‑on experience with cloud platforms (AWS, GCP, or Azure).
• Familiarity with workflow management systems (Snakemake, Nextflow, Cromwell).
• Familiarity with NGS platforms (Illumina, Pac Bio, Oxford Nanopore).

Application Date: Priority consideration will be given to candidates…