Bioinformatics Engineer, Clinical Genomics Pipelines
Build production NGS pipelines for oncology and inherited-disease clinical sequencing assays.
About the role
The company develops and runs regulated NGS assays used for oncology profiling and inherited-disease testing. This role supports the clinical genomics workflows used by assay development, laboratory operations, QA, and reporting teams. You will improve pipeline reliability, validation support, version control, and troubleshooting in a regulated diagnostics environment.
- Team: Bioinformatics engineering team of 5 supporting assay development and clinical operations
- Stage: Scaling molecular diagnostics company expanding oncology and inherited-disease test volume
- Reporting line: Senior Manager, Bioinformatics Engineering
- Experience: MS with 4+ years, or BS with 6+ years, building NGS or clinical genomics pipelines
- Rhythm: Hybrid with scheduled onsite collaboration in RTP and occasional weekend validation support
Responsibilities
- Develop, test, and maintain NGS workflows for FASTQ processing, alignment, variant calling, annotation, QC reporting, and sample-level traceability.
- Partner with assay development and lab operations to move workflow changes from development into production without losing version control, auditability, or reproducibility.
- Support analytical validation, CAP/CLIA documentation, change control, release notes, and troubleshooting when pipeline behavior affects reported results.
Requirements
- MS with 4+ years, or BS with 6+ years, of professional experience building bioinformatics pipelines for NGS, genomics, molecular diagnostics, or related regulated workflows.
- Strong Python and shell scripting skills, plus production experience with Nextflow, WDL, Snakemake, or a comparable workflow system.
- Practical familiarity with standard genomics tools and file formats such as BWA, GATK, samtools, Picard, FASTQC/MultiQC, BAM/CRAM, VCF, FASTQ, and QC metrics.
- Experience with Docker or other containerized workflows, CI/CD testing, version control, and reproducible analysis practices.
- Ability to investigate pipeline artifacts, failed runs, sample swaps, reference-data changes, annotation differences, and edge cases that matter in clinical reporting.
- Clear communication style for working with laboratory, QA, regulatory, and assay development stakeholders.
Preferred qualifications
- Experience supporting CAP/CLIA, NYS, FDA-facing, or similar clinical validation documentation.
- Experience with CNV, structural variant, repeat expansion, or hard-to-map genomic regions.
- AWS, Kubernetes, or workflow orchestration experience in a production environment.
Technical stack
- Python
- Bash
- Nextflow/WDL/Snakemake
- Docker
- AWS
- BWA/GATK/samtools
- Picard/FastQC/MultiQC
- VCF/BAM/FASTQ
- CAP/CLIA documentation
What we offer
- Base salary: $138k - $165k
- Equity / upside: Modest equity plus annual operational bonus.
- Benefits: Medical, dental, vision, 401(k), disability coverage, and relocation support.
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