Bioinformatics Systems Analyst (Sequencing Technology)

Lawrence Berkeley National Laboratory
Job Location
Walnut Creek, CA 94598
Job Description

Bioinformatics Systems Analyst (Sequencing Technology) - 80318
Organization:  GN-Genomics

The DOE Joint Genome Institute (JGI) in Walnut Creek, CA (a division of the Lawrence Berkeley National Lab) has an exciting opportunity available for a Bioinformatics Systems Analyst to perform large-scale data analysis and develop computational tools for R&D projects surrounding genome, transcriptome and chromatin characterization.

This role will evaluate the nature of biological challenges, design of molecular biological approaches and short read sequencing data, as well as thoroughly analyze DNA sequence data produced by next generation sequencing machines and various library types. Will develop and implement analysis pipelines, and provide technical and analytical data interpretation. Will also be responsible for improving existing data analysis tools and implement new tools for general use.

This position will have a significant role in defining biological significance of the data, will work with various JGI groups on data analysis projects and facilitate transfer of knowledge of technologies and applications to JGI staff. May also provide custom analysis support to external collaborators. Will report to the Sequencing Technology Group analysis work lead.

Key Responsibilities:
Sequence Analysis and Interpretation
• Perform quality analysis of sequence data and assist others in interpretation of analyzed data.
• Extract new biological insights and phenomenon from the analyzed results.
• Independently and proficiently utilize assembled genomes, various alignment tools, visualization tools, and other genome interrogation and analysis software.
• Be familiar with the different types of data and approaches for chromatin (epigenetic) interrogation, transcriptome characterization and genome assembly.
• Provide data quality feedback to wet-lab scientists and sequencing team members.
• Provide clear and concise professional reports on data analysis and results.
• Present technical and analytical status in weekly meetings.
• Contribute to publications on experimental data generated by the new sequencing approaches.

Bioinformatics Tool Adaptation and Improvement
• Adapt and improve bioinformatics tools to process sequencing data generated by various R&D library types and projects.
• Participate in the design and development of new tools for new R&D projects.
• Refine and improve existing analytical tools.
• Design and build new tools to analyze sequences of various research projects.
• Troubleshoot system and data analysis problems and provide feedback on areas of improvement for existing tools.
• Provide technical support to detect issues and improve library protocols.
• Provide high quality documentation for newly developed software and approaches.

In addition to the above, the following are responsibilities for the higher analyst level:
• May provide functional and technical guidance to others, including assisting co-workers in problem resolution.


• Demonstrated experience processing large volumes of data, whole-genome data analysis, phylogenetics and comparative genomics
• B.S. in Bioinformatics, Computer Science, Biology or a related field plus typically at least 2 years of experience in genome bioinformatics, or an overall equivalent combination of education and experience; Master’s/ Ph.D. preferred
• Experience with the collection, recording and analysis of large-scale experimental data
• Knowledge of genome assemblers, DNA sequencing, short read alignment programs and large-scale data analysis
• Knowledge and experience with standard bioinformatics methods and tools, including sequencing databases
• Familiarity with various molecular biology procedures, including DNA sequencing, PCR and cloning
• Knowledge of Perl/Python, C/C++, Java or others in a Unix environment; familiarity with software engineering and web-based interface
• Experience with SQL, MySQL, Oracle or other RDBMs
• Experience with database structure and management
• Familiarity with statistical tools, applied statistics and interpretation of data
• Experience applying machine learning, pattern recognition, or modeling to scientific problems
• Demonstrated analytical skills sufficient to troubleshoot system and data analysis problems and make recommendations
• Proficient organizational and record-keeping skills
• Effective oral and written communication and interpersonal skills
• Ability to work independently and as a team member in a diverse team environment
• Ability to handle multiple tasks in parallel while working on a large number of projects
• Ability to follow laboratory safety guidelines
• Preferred - Knowledge and experience with laboratory DNA sequencing technologies and genetics, or related field or equivalent experience preferred.
• Preferred - Experience in a multi-disciplinary scientific or production environment.

In addition to the above, the following are qualifications for consideration at a higher job classification level:
• B.S. in relevant field plus typically at least 5 years of experience in genome bioinformatics, or an overall equivalent combination of education and experience
• Expertise with genome assemblers, DNA sequencing, short read alignment programs and large-scale data analysis
• Proficient programming skills
• Demonstrated ability to successfully and independently perform work aligned with the project goals and objectives

Notes: A single 1-year term appointment will be hired at the job classification level appropriate to the successful candidate’s relevant breadth and depth of experience. Possibility of renewal and and/or conversion to career is based upon satisfactory job performance, continuing availability of funds, and ongoing operational needs.

Work location: Work will be performed at the DOE Joint Genome Institute (JGI) in Walnut Creek, CA. May require occasional travel, weekend, and after-hours work. A background check is required. Multiple positions may be hired.

How to Apply

Apply directly online at and follow the on-line instructions to complete the application process.

About Our Organization

About Us
Rapid technological advances in genomics have transformed modern biology. From its inception, the Department of Energy Joint Genome Institute has been at the forefront of large-scale sequence-based science. Learn more at  This position is part of the Sequencing Technologies Group that provides end-to-end support for the DOE JGI production sequencing activities. Our group applies state-of-the-art automation-based processing technologies coupled with high throughput sequencing operation to support our global DOE research community. Learn more about Genomic Technologies at the JGI (

Berkeley Lab is an Equal Opportunity/Affirmative Action Employer. All qualified applicants will receive consideration for employment without regard to race, color, religion, sex, national origin, disability, age or protected veteran status.

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