Bioinformatics Software Engineer 2 in San Diego, California

Illumina’s Customer Collaboration & Innovation (CCI) team transforms the relationship between top-tier customers and our Product Development organization, and we are looking for a select individual to join the team as a Bioinformatics Software Engineer 2.  The team works externally with a small number of Illumina’s top customers to design and deploy workflow solutions that meet their business needs.  Those solutions will span the complete genome sequencing space from sample accessioning and library prep, through sequencing and secondary analysis, and into tertiary analysis and reporting.  The solutions will incorporate the best components that Illumina has to offer with the specific requirements of the customer in a seamless whole. 

The Bioinformatics Software Engineer 2 will have opportunities to be part of a customer interface team for these top-tier customers.  As such, this person must be an excellent communicator and listener and able to effectively collaborate with internal and external teams.  The Software Engineer 2 will also interact very actively with internal SW development teams, be responsible for beta product testing, support the debug and resolution of customer issues and participate in proof of concepts and Illumina solution evaluations with potential customers.

The applicant must have a technical background in bioinformatics and software development, and the ability to quickly develop prototype workflows and components to achieve a customer’s needs.  The applicant must also be comfortable working in Linux environment with computing onsite with a HPC and in the Cloud, which would include AWS, Azure and/or Google. 

The CCI team and its customer base is spread across the world, so there may be a need for off-hours interaction in meetings and other day-to-day forums.  When worldwide circumstances allow it again, the role may also involve some travel to customer sites for collaboration, deployment, and debugging activities. A successful candidate must be willing to work in a fast-paced environment and be ready to adapt to quick changes as customer issues or needs arise.

Familiarity with Illumina’s software products would be extremely beneficial for the applicant, and might include the following:  BaseSpace Sequence Hub (BSSH) and DRAGEN

Job Responsibilities

  • Troubleshoot Illumina’s bioinformatics product offerings in the hands of customers

  • Collaborate with the customer to develop solutions in large scale genomic data management, virtualization and cloud-based system deployment through on Illumina software and infrastructure

  • Work in close communication with Illumina R&D to help deliver and test solutions, and troubleshoot issues to enable rapid resolution regarding the deployment of the customer methods onto Illumina architecture

  • Participate in Beta and Early Access evaluations of Illumina solutions with key customers.

  • Create or configure interface components to tie Illumina informatics offerings together with components created or pre-selected by customers to deliver e2e solutions

  • Feed the needs of customers back into the Illumina development organizations and work closely with R&D to drive improvements in product offerings and get new pipelines and tools to customers

  • Support product testing of new Illumina product offerings into existing workflows to proactively identify problem areas and opportunities for improvement

  • Help collect accurate technical descriptions and relevant data associated with bugs in Illumina informatics and software components to enable rapid resolution for customers

Listed responsibilities are an essential, but not exhaustive list, of the usual duties associated with the position.  Changes to individual responsibilities may occur due to business needs.

Technical Requirements

  • BSc/MS in Computer Science, Bioinformatics, or related field.

  • 2+ years of work experience with C, C#, C++, Javascript, Python, Perl, R or similar software languages

  • Strong knowledge of the Linux operating system

  • Familiarity with Cloud architecture and concepts (EC2, Lambda, RDS, S3, SQS, SNS, SWF, Blob Storage, Batch etc.)

  • Have an understanding of the basics of next-generation sequencing (NGS) workflows and analysis pipelines for various sample types

  • Working knowledge of common genome analysis toolkits like GATK, as well as standard data formats common in the genomic analysis industry like FASTQ, FASTA, BCL, VCF, BAM, etc.

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 requires proof of COVID vaccination for all U.S.-based employees (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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