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Bioinformatics Software Engineer

Company: Fulgent Genetics
Location: Temple City
Posted on: January 17, 2020

Job Description:

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 challenge genomics problems, such as, haplotype phasing, de novo assembly, structure variation detection, and copy number variation. The ideal candidate will have experience on developing and implementing NGS data analysis pipeline using techniques such as sequence alignment, text indexing and searching, genome assembly, graph algorithms, combinatorial optimization and probability theory. Responsibilities * Analyze internally generated 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 internally 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. Qualifications * 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)Strong hands-on skills in relevant programming languages (e.g., R, Python, PERL, UNIX/Linux, UNIX bash shell scripting, JAVA, C/ C++), statistical software, visualization tools, and relevant R/ Bioconductor packages. * Familiarity with more than one of the following; analyzing next- generation sequencing (NGS) data (e.g., single-cell genomics), functional genomics, facility with statistics for big data analysis, or multi-omics data integration. * Experience in developing genomics pipelines and containerizing workflows. * 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. * Experience in machine learning, experience with atypical datasets, and application or development of single-cell sequencing analysis algorithms is a plus. Fulgent Genetics is an Equal Opportunity Employer. To apply please email cover letter and resume to ****************************

Keywords: Fulgent Genetics, Los Angeles , Bioinformatics Software Engineer, IT / Software / Systems , Temple City, California

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