Senior Bioinformatics Engineer responsible for designing, building, and operating production-grade, end-to-end bioinformatics pipelines that process and interpret large-scale genome cohorts. The role involves deep expertise in genome assembly, variant calling, structural-variant calling, haplotype phasing, and pangenome analysis, with the ability to select, adapt, and benchmark state-of-the-art algorithms.… Requires proficiency in Python and compiled languages (C++/Rust/Go), containerization (Docker/Singularity), workflow managers (Nextflow/Snakemake/WDL), and cloud environments (AWS/GCP). The position combines applied research—exploring AI approaches for biological insight—with continuous improvement of algorithms, code, and computational infrastructure, while mentoring junior staff in a startup environment.
wdl jobs in San Diego
Build and maintain computational pipelines for sequence analysis and genotyping in HPC and cloud environments, using tools like PLINK, GATK, and BEAGLE. Perform quality control on data inputs and outputs, document work meticulously, and develop new pipelines under supervision by selecting and testing computational approaches.… Requires expertise in Bash scripting, bioinformatics software, Linux, cloud platforms (AWS EC2, All of Us Research workbench), and programming languages (R, Python), plus strong written and verbal communication skills.
The Bioinformatics Test Engineer will design and execute comprehensive testing strategies for NGS (Next Generation Sequencing) data pipelines, including alignment, variant calling, and annotation workflows. Responsibilities include data validation, regression testing, automated test script development in Python, and collaboration with CI/CD pipelines and cloud-based systems.… The role requires deep knowledge of NGS file formats (FASTQ, BAM, VCF), proficiency in Python scripting, hands-on experience with Git and CI/CD tools, and familiarity with cloud platforms (AWS/GCP/Azure) to ensure data accuracy and pipeline reliability.