RESPONSIBILITIES:
Organization: GN-Genomics Division

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. Under general supervision, will serve as a Systems Analyst (level 2 or 3) to develop computational tools for the assembly of microbial genomes using 2nd-generation (Illumina HiSeq) and 3rd-generation (Pacific Biosciences and others) sequence data. Will play a central role in developing a high-throughput sequencing and analysis pipeline that is capable of producing 1000's of high quality `finished' microbial genome sequences per year. Will work closely with experimental biologists and other bioinformaticians to achieve these goals. Position will report to the head of the Genome Assembly Group.

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:
Essential-

• Perform primary analysis of sequence data including quality control and handling of multiplexed samples, and provide feedback to experimental biologists.
• Use publicly available and in-house developed software to develop high-throughput computational strategies for assembly of `draft' quality microbial genome sequences using second generation (illumina HiSeq) data.
• Develop computational strategies for improving and `finishing' microbial genome assemblies using 3rd generation sequencing technologies (e.g. Pacific biosciences)
• Develop computational tools to evaluate the accuracy and completeness of microbial genome assemblies, and to compare different assembly strategies.
• Evaluate the cost and computational resource demands of different assembly strategies to ensure suitability for the analysis of 1000's of genomes per year.
• Work closely with bioinformaticians in the production informatics department to develop the most promising assembly strategies into production-scale computational pipelines.
• Perform frequent improvement of assembly strategies by evaluating novel genome assembly algorithms, and sequence data types. Provide feedback to experimental biologists on the suitability of new sequence data types for genome assembly.
• Investigate alternative genome assembly strategies as new and improved sequencing technologies and assembly algorithms become available (e.g. assembly using only 3rd generation sequence data).
• Troubleshoot systems and data problems and exercise independent judgment to select appropriate solutions.
• Present progress at internal group meetings.

Marginal-

• Apply the tools and insights gained from microbial genome assembly to more complex sequence datasets (e.g. eukaryotic genome and metagenome assembly).
• Assist with the assembly of whole genome amplified DNA from single cells.

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 more complex systems and data analysis problems.

REQUIREMENTS:
Essential-

• Bachelor's degree in Biology, Bioinformatics, Computer Science or related field with a minimum of two years of work experience, or an equivalent combination of education and experience. Advanced degree preferred.
• Knowledge of standard bioinformatics methods preferably including tools for genome assembly.
• Experience in computational analysis of large next-generation sequence datasets.
• Experience programming with Perl / Python or similar language in a UNIX environment.
• Strong problem-solving, decision-making, and analytical skills to independently make sound judgments and recommend creative solutions to moderately complex problems.
• Strong interpersonal, communication, and presentation skills.
• Detail-oriented with strong organizational skills to address user needs in an effective and timely manner.

Marginal-

• Experience programming in a parallel environment strongly preferred

Essential requirements for the Systems Analyst 3 - In addition to the required duties for a level 2, the Analyst 3 will have:

• Bachelor's degree in Biology, Bioinformatics, Computer Science or related field with a minimum of five years of work experience, or an equivalent combination of education and experience.
• Demonstrated expertise processing large volumes of data, whole-genome data analysis, phylogenetics, and comparative genomics.
• Ability to troubleshoot complex systems and data analysis problems.

HOW TO APPLY:
Apply directly online at:
http://bit.ly/lbl73419Bioinformatics and follow the on-line instructions to complete the application process.

POLICY:
Berkeley Lab is an affirmative action/equal opportunity employer committed to the development of a diverse workforce.