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 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, 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, design and development of 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 supported by the Biological and Environmental Research (BER) program, JGI advances BER's mission to achieve a predictive understanding of complex biological, Earth, and environmental systems in support of the nation's energy and infrastructure security. Through world-class capabilities in genome sequencing, synthesis, transcriptomics, metabolomics, natural products, and data science, JGI supports cutting-edge research on plants, fungi, algae, microorganisms, and microbiomes. JGI is headquartered in Berkeley, CA at Berkeley Lab's Integrative Genomics Building (IGB) (Virtual Tour).

This position has an anticipated start date of July 1, 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!

Why join Berkeley Lab?

We invest in our employees by offering a total rewards package you can count on:

• 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

What You Will Do:

• 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., * Appointment Type: This is a full time, exempt from overtime pay (monthly paid), 2 year (benefits eligible), Term appointment with the possibility of extension or conversion to Career appointment based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs., Misconduct Disclosure Requirement: As a condition of employment, the finalist will be required to disclose if they are subject to any final administrative or judicial decisions within the last seven years determining that they committed any misconduct, are currently being investigated for misconduct, left a position during an investigation for alleged misconduct, or have filed an appeal with a previous employer. Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision:https://www.dol.gov/ofccp/PayTransparencyNondiscrimination.html under 41 CFR 60-1.4. Click here:https://www.dol.gov/ofccp/regs/compliance/posters/ofccpost.htm to view the poster and supplement: "Equal Employment Opportunity is the Law." Equal Employment Opportunity: Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, sexual orientation, gender identity, national origin, disability, age, or protected veteran status. Berkeley Lab is in compliance with the Pay Transparency Nondiscrimination Provision : https://www.dol.gov/ofccp/PayTransparencyNondiscrimination.html under 41 CFR 60-1.4. Click here: https://www.dol.gov/ofccp/regs/compliance/posters/ofccpost.html to view the poster and supplement: "Equal Employment Opportunity is the Law."

• 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.
• Demonstrated 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.
• Demonstrated capacity 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 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 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, PacBio, Oxford Nanopore).

• Salary Range: This position has a budgeted salary range of $117,132 - $146,400 annually, which fits within the full salary range of $117,132 - $197,676 annually for job code C70.2. It is not typical for an individual to be offered a salary at or near the top of the range for a position. Salary will be commensurate with the final candidate's qualification and experience, including skills, knowledge, relevant education, certifications, and aligned with the internal peer group.
• Background Check: This position is subject to a background check. Any convictions will be evaluated to determine if they directly relate to the responsibilities and requirements of the position. Having a conviction history will not automatically disqualify an applicant from being considered for employment.