Sr. Bioinformatics Scientist, Production Data Engineer

Illumina | San Diego, CA

Posted Date 5/13/2022
Description As a Sr. Bioinformatics Scientist, your primary responsibility is to enable the data analysis and processing and successful delivery of data within a cloud system to meet project based KPIs for Illumina’s partnership with Nashville Biosciences, and future large-scale data generation projects. This role will play a key part of the establishment and scaling of data analysis workflows, primarily using Illumina cloud software and tools such as DRAGEN, as well as running and monitoring pipelines in production and working on any analysis failures or NGS samples that have not met QC metrics. The role will be a key interface to two or more sequencing labs that will deliver NGS data into the Illumina cloud system for analysis, and your responsibilities will include joint resolution of any samples that need resequencing or other actions by the originating lab. Finally, the analysis data will be periodically published, along with matching clinical data, to a consortium of stakeholders. Tasks and Responsibilities: Manage, monitor and run bioinformatics workflows in a production environment on the Illumina Connected Analytics cloud system. Manage and perform root-cause analysis troubleshooting for data analysis failures. Work closely with key stakeholders and colleagues across the globe to meet project KPIs. Contribute to the building, development and testing of new pipelines and workflows. Ensure all data is maintained in a secure way, following best practice data security practices in the cloud . Execute on periodic cross-provider quality measurements to ensure consistent and high-quality results. Provide performance updates and trending data for the project for key stakeholders, both in written format and through oral presentations. Deliver periodic tranches of analysis data combined with matching structured clinical data to consortium members, along with aggregate statistics, quality measures, and other relevant metrics. All listed tasks and responsibilities are deemed as essential functions to this position; however, business conditions may require reasonable accommodations for additional task and responsibilities. Educational Background & Experience: Bachelors, Masters, or PhD in Bioinformatics or a related field and 5+ years of relevant experience Essential Excellent understanding of bioinformatics, genomics, sequence analysis and related disciplines. Experience with Bioinformatics algorithms for processing of NGS data, preferably for Whole Genome sequencing data, such as DRAGEN, BWA/GATK or equivalent Demonstrated experience in handling and troubleshooting NGS data Demonstrated capability to work with linux, bash and command line tools Knowledge of one or more programmatic languages common in Bioinformatics, such as Python, R, and Ruby Familiarity with AWS Services, container services (e.g. Docker), and database warehouses (e.g. Snowflake) Experience collaborating with 3rd-party service providers Extreme attention to detail Preferred A strong understanding of cloud systems for processing NGS data Knowledge of workflow languages such as CWL, NextFlow, Snakemake Familiarity with relational databases including SQL Strong written and oral communication skills Ability to work in a team environment Experience writing automated tests or creating QC dashboards Concerns regarding COVID-19 continue as positive cases are experienced in the communities in which we operate. Please be aware that, as a condition of employment, Illumina may require proof of COVID vaccination in accordance with local statutory requirements (subject to limited exceptions) beginning November 1, 2021. At Illumina, we strive to foster a diverse and inclusive workplace by cultivating an environment in which everyone contributes to our mission. Built on a strong foundation, Illumina has always been rooted in openness, collaboration, and seeking alternative views and perspectives to propel innovation in genomics. We are proud to confirm a zero-net gap in pay, regardless of gender, ethnicity, or race. We also have several Employee Resource Groups (ERG) that deliver career development experiences, increase cultural awareness, and demonstrate our collective commitment to diversity and inclusion in the communities we live and work. We are proud to be an equal opportunity employer committed to providing employment opportunity regardless of sex, race, creed, color, gender, religion, marital status, domestic partner status, age, national origin or ancestry, physical or mental disability, medical condition, sexual orientation, pregnancy, military or veteran status, citizenship status, and genetic information. If you require accommodation to complete the application or interview process, please contact To learn more, visit:

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