Bioinformatics Systems Analyst 2/3 - Sequence Analysis

Organization: 
Lawrence Berkeley National Laboratory
Job Location: 
Walnut Creek, CA
Job Description: 

Bioinformatics Systems Analyst 2/3 - Sequence Analysis - 75414
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 an experienced Bioinformatics Systems Analyst to perform DNA sequence analysis for production, and research and development projects. Duties include performing thorough quality and assembly analysis of DNA sequence data produced by the new generation of sequencing machines. Focus will be on analysis of metagenomic, plant, fungal, and microbial sequence data. Will implement improvements to data analysis systems, assess and improve existing tools, develop new tools for general use, and provide technical and analytical interpretation of data. May also provide custom analysis support to external collaborators and supervise non-exempt group members. Will report to the QC/QA Group Lead.

The selected candidate will be hired at the Analyst 2 or 3 classification depending upon the candidate's level of experience and qualifications.

Specific Job Duties
Sequence Analysis and Interpretation-
• Perform quality analysis of sequence data and assist others in interpretation of analyzed data.
• Define quality metrics for assessing library and sequencer performance.
• Utilize genome assemblers (such as Velvet, Newbler etc), visualization tools, and other genome assembly and analysis software.
• Evaluate assembly results and improve genome assemblies methods.
• Provide high quality data to collaborators.
• Provide clear and concise professional reports.
• Work closely with scientists and production staff to improve production line quality.
• Present technical and analytical status in meetings.

Bioinformatics Tool Development-
• Develop and improve tools to evaluate quality of data generated by various sequencing platforms and library types.
• Refine and improve existing analytical tools.
• Design and build new tools to analyze assembled 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 implement new sequence analysis pipelines.
• Provide high quality documentation for newly developed software and approaches.

Essential Duties for the Analyst 3 - In addition to the required duties for a level 2, the Analyst 3 will:
• Work at a higher level of independence and responsibilities in carrying out assignments.
• Develop and implement substantial, known or novel, computational methods to improve the analysis capabilities and output of the group.
• Troubleshoot complex systems and data analysis problems.

Requirements: 

Key Success Factors
Essential-
• Typically requires a B.S. in Biology, Bioinformatics, Computer Science or a related field and at least two years of experience in genome assembly or bioinformatics; or an equivalent combination of education and experience.
• Strong background in biology and biochemistry.
• Strong background in bioinformatics, mathematics, molecular biology and genomics.
• Demonstrated experience applying statistics to analyze large biological datasets.
• Proficiency with programming languages including PERL, C/C++, Java or others in a Unix environment.
• Demonstrated analytical skills sufficient to troubleshoot system and data analysis problems and make recommendations.
• Strong 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 multi-disciplinary team environment.
• Ability to handle multiple tasks in parallel while working on a large number of projects.
• Ability to follow laboratory safety guidelines.
• Experience with distributed computing.

Marginal-
• Knowledge and experience with laboratory DNA sequencing technologies and genetics, or related field or equivalent experience preferred.
• Some experience with database structure and management.
• Experience applying machine learning, pattern recognition, or modeling to scientific problems.
• Experience in a multi-disciplinary scientific or production environment.

Essential Qualifications for the Systems Analyst 3 - In addition to the required qualifications for a level 2, the Analyst 3 will have:
• Bachelor's degree in Biology, Life Sciences, Bioinformatics, Computer Science or related field with a minimum of five years of experience in genome assembly or bioinformatics; or an equivalent combination of education and experience.
• Advanced SQL, Perl or Java software skills.
• Ability to troubleshoot complex systems and data analysis problems.

Berkeley Lab is an Affirmative Action/Equal Employment Opportunity employer committed to the development of a diverse workforce.

Contact Information: 

How To Apply
Apply directly online at http://bit.ly/lbl75414Genomeweb and follow the instructions to complete the application process.