Bioinformatics Engineer

Job Location: 
San Diego - CA
Competitive base, bonus plus equity

Full benefits

Job Description: 

The Bioinformatics Engineer is responsible for the design and implementation of a sequencing analysis pipeline at Sequenom. More specifically, the candidate will:

Develop tools for automating DNA sequence assemblies and sequence data quality reporting.

Develop and maintain high performance computational platform for sequence data analysis pipeline.

Develop and maintain database infrastructure and LIMS for the sequencing data.

Perform appropriate documentation and testing
Support multiple-site operation.


The Ideal Candidate will have:

Master’s degree in molecular biology, bioinformatics, or related field; Ph.D. preferred

3 years of experience in a high-throughput sequencing environment and experience with next-generation sequencing and data analysis.

Knowledge of nucleic acid hybridization kinetics and properties, PCR kinetics and properties.

Familiarity with genomic browser(s) content and functionality.

Demonstrated expertise with PERL and shell scripting, and experience with Java.

Experience with unit testing.

Demonstrated expertise with relational database systems - SQL server, Oracle, MySQL, PostgreSQL.

Experience with statistical software, such as R.

Experience developing software for research purposes.

Broad knowledge of UNIX/Linux.

Ability to troubleshoot research-grade software, both internally developed as well as third-party provided.

Ability to present information in a clear and concise manner to a multidisciplinary team of scientists, engineers and programmers.

Experience with high-performance computing environments. Proven experience with a mainstream cluster job manager – SGE, LSF/OpenLava, PBS/Torque.

Proven experience with deployment of a data analysis pipeline in a distributed computing environment.

Contact Information: 

Apply online at


Email resumes directly to

About Our Organization: 

Sequenom Laboratories, a wholly-owned subsidiary of Sequenom, Inc., is a CAP accredited and CLIA-certified molecular diagnostics laboratory, dedicated to the development and commercialization of laboratory-developed tests (LDTs) for prenatal and ophthalmic diseases and conditions.
As a life sciences company, Sequenom (NASDAQ: SQNM) has a guiding vision: To improve healthcare by providing revolutionary genomic and genetic analysis solutions for the clinical research and molecular diagnostic markets.

What makes this vision a reality? Our deep commitment to "Quality of Science." For us, only the highest quality is acceptable. Sequenom team members thrive in a "science first" environment where ideas and innovation are part of daily life. This is your opportunity to work on cutting-edge science that is revolutionizing patient care.

Our innovation-driven culture means life at Sequenom is fast-paced, dynamic, and fun with rewarding benefits and performance rewards. With a clear vision for the future, all employees have the opportunity to make a difference and are encouraged to share new ideas. We foster a collaborative work environment and encourage curiosity at all levels. Our corporate headquarters is located in the heart of San Diego’s life sciences community, less than a mile from the beach.