Software Developer (Genomics Analysis Team)
About The Position
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 supporting large-scale genomics research. This role focuses on supporting the automation of a diverse set of genome analysis pipelines and their associated quality control processes. It is central to building the Institute’s analytical capabilities, enabling growth from processing tens to hundreds of thousands of samples in support of exciting, large-scale scientific initiatives. This hands-on role involves building and maintaining next-generation sequencing (NGS) data processing pipelines, designing 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. You will troubleshoot production systems, optimize database performance and queries, support ad-hoc analyses for research staff, and produce clear, high-quality technical documentation. The JGI’s mission is to provide the global research community with access to the most advanced integrative genome science capabilities in support of the DOEs research mission to solve the world’s evolving energy and environmental challenges. The JGI supports projects in genome sequencing, synthesis, transcriptomics, metabolomics, and natural products in plants, fungi, algae, and microorganisms. This position is headquartered on the Lab’s main site at the Integrative Genomics Building (IGB) (Virtual Tour). This position has an anticipated start date of April 13, 2026. We’re here for the same mission, to bring science solutions to the world. Join our team and YOU will play a supporting role in our goal to address global challenges! Have a high level of impact and work for an organization associated with 17 Nobel Prizes!
Requirements
- A Bachelor’s Degree (or equivalent knowledge/training) in Operations Research, Systems Engineering, Computer Science, or a related discipline and a minimum of 5 years of professional software engineering experience in industry or production environments or an equivalent combination of education and experience.
- Demonstrated capacity to manage multiple projects and competing priorities.
- Strong proficiency in Python using pandas, matplotlib, data processing libraries, and RESTful web service development with FastAPI.
- Experience with relational databases (MySQL/PostgreSQL) in Unix environments, including query optimization and schema design.
- Hands-on experience with Git workflows, proficiency in BASH/shell scripting for automation, and an ability to create dynamic web pages using HTML, CSS, and JavaScript.
- Demonstrated track record of maintaining and evolving complex codebases.
- Strong analytical skills including the ability to identify problems, troubleshoot, and demonstrate good judgement 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 skills including experience collaborating with an interdisciplinary research team.
Nice To Haves
- Experience with CI/CD pipelines and automated testing.
- Experience with Linux system administration with 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, PacBio, Oxford Nanopore).
- Experience applying machine learning, pattern recognition, or modeling techniques to scientific problems.
Responsibilities
- 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 data visualization and pipeline monitoring.
- Maintain and enhance a substantial codebase (Python) 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 genomic analyses in collaboration with scientific staff.
Benefits
- Exceptional health and retirement benefits, including pension or 401K-style plans
- A culture where you’ll belong - we are invested in our teams!
- In addition to accruing vacation and sick time, we also have a Winter Holiday Shutdown every year.
- Parental bonding leave (for both mothers and fathers)
- Pet insurance
Stand Out From the Crowd
Upload your resume and get instant feedback on how well it matches this job.
What This Job Offers
Job Type
Full-time
Career Level
Mid Level
