Bioinformatics Software Engineer, Java Specialist

Fulgent Genetics
United StatesCaliforniaEl Monte (Optional Remote)



Fulgent is a leader in genetic and genomic clinical testing, a publicly traded company located in Los Angeles, California. We are a technology-driven company with extensive academic/clinical experience and capabilities in Next Generation Sequencing and bioinformatics. This distinction has advanced us to the forefront of the rapidly advancing genetic and genomic testing industry.

Fulgent's unique chemistries and superior proprietary bioinformatics pipeline has propelled our explosive growth in recent years. We offer the most expansive set of clinical genetic tests in the world, including 22,000+ single gene tests, 900+ preset panels, rearrangement testing, clinical exome/trios, whole exome/trios, whole genome and our All-in-One reflex test. We are a CLIA and CAP accredited laboratory. Fulgent has state-of-the-art clinical, sequencing and bioinformatics tools, including the latest Illumina sequencers such as the NovaSeq.


The Bioinformatics Software Engineer will be responsible for the development, deployment, integration, and support of bioinformatics applications for genomic testing operations. This position will lead the development and integration of genomic data analysis pipelines to solve challenging germline or somatic genomics problems such as haplotype phasing, de novo assembly, structure variation detection, and copy number variation. The ideal candidate will have substantial strength in Java development and Java implementation and optimization. More emphasis will be placed on bringing projects from 99% to 100% completion using QC, error catches, memory optimization, and database integration. Projects will vary widely and growth opportunities will be made available.


Analyze NGS sequencing data.
Work with Curation, R&D, Bioinformatics Integration, and Software Engineering to understand applications and requirements.
Design and develop new data analysis pipeline processes using Fulgent-developed algorithms.
Design and develop software for applications in haplotype phasing and assembly.
Work with internal and/or external users to develop and support customized solutions based on our core products.
Work closely with the assay development, clinical, wet lab, and IT teams to bring new assays into production.
Gather requirements, design high-level workflows, anticipate business needs, and estimate timelines for bioinformatics projects.
Create and improve existing testing and deployment frameworks for bioinformatics software development.
Optimize existing systems (pipelines, databases, etc.) to improve scalability and maintainability.
Contribute to the development of software for new assay implementation.
Mentor junior developers in best coding practices and general career development.



PhD in computer science, bioinformatics or related field with 0-3 years of postdoctoral experience or MSc in computer science, bioinformatics or related field with at least 5 years of post-graduate experience.
Strong experience with tool development for NGS DNA sequence analysis.
Hands on experience with NGS data analysis tools (e.g. bwa, samtools, SNP Graph, RefHap). Hands-on skills in Java primarily, but some prototyping work could be in python or R.
Some familiarity with next-generation sequencing (NGS) data, germline or cancer genomics, facility with statistics for big data analysis, multi-omics data integration.
Some experience in developing genomics pipelines and containerizing workflows but skills outside genomics will be considered relevant.
Experience with continuous integration and deployment.
Experience with API query language.
Experience with DevOps.
Experience with analytics and big data systems.
High competency with version control systems like Git.
Must enjoy working in a multi-disciplinary and collaborative environment.
Ability to troubleshoot both individually and as part of a team.
Excellent oral and written skills with the ability to communicate in an open, transparent, timely and consistent manner.

Start date

As soon as possible

How to Apply

Apply directly using the provided URL or email recruiter Deanna Tremblay for more information


Deanna Tremblay