Bioinformatics Specialist

Sequenom, Inc.
Job Location: 
San Diego, CA
Competitive salary, bonus, stock options
Job Description: 

Join the CLIA laboratory that is dedicated to improving healthcare through revolutionary genetic analysis solutions. The rapidly growing Sequenom Center for Molecular Medicine is on the forefront of ground-breaking clinical diagnostic tests. Sequenom Center for Molecular Medicine, a wholly-owned subsidiary of Sequenom, is a CLIA-certified specialty reference laboratory dedicated to the development and commercialization of laboratory-developed genetic testing services for prenatal and eye conditions. Headquartered in San Diego, with offices located around the world, we provide the opportunity to collaborate with talented and dedicated scientific leaders while developing and expanding your own career. We know our strength and competitive advantage comes from our people so we strive to maintain a motivated team and an environment that supports diversity, encourages creativity, and most importantly, fosters innovation. Our employees are rewarded with excellent compensation and top-notch benefits. Consider joining the Sequenom CMM team, where you can help make an impact in revolutionizing medical technology.

The Bioinformatics Specialist is responsible for developing and extending data analysis pipelines running on a HPC cluster, performing analyses of sequencing data such as SNP calling and structural variant calling as pertaining to prenatal diagnostics studies and assisting with the development, extension, and support of LIMS solutions for storing and reporting experimental and analytical results.

• Monitor and trouble-shoot analysis pipeline in an HPC environment.
• Perform NGS data analysis for SNP calling, structural variant calling, and indel analyses.
• Participate in the design and development of analysis pipeline running on a local or cloud-based cluster.
• Participate in development and support of laboratory information management systems (LIMS).
• Develop scripts to extract results from instrument-generated files and to store data in a database.
• Work closely with analytical team to provide access to data from instruments and analysis.
• Provide reports and analysis information to management to aid in decision making on the development of new products.


• Master degree in Computational Biology/Bioinformatics, Computer Science or related field and or equivalent work experience in biotech industry
• Experiences with public domain tools of NGS data analysis: GATK2, Bowtie, BWA, SOAP, Casava, Samtools, Bedtools, BreakDancer
• Demonstrated strong programming/scripting skills (E.g., Linux Shell, Perl) with experiences of High Performance Clusters and/or AWS
• Experience with R, Java, and C++ is a plus.
• Proficient with SQL and interacting with relational databases (Oracle, MySQL, SQL Server).
• Good understanding of software development processes.
• Strong writing, organization and communication skills.


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