# Bioinformatics Engineer, Clinical Genomics Pipelines

Live page: https://affinitytalent.bio/jobs/bioinformatics-engineer-clinical-genomics

## Role summary

- Scaling molecular diagnostics company
- Research Triangle Park, NC, US
- Hybrid · Mid-level
- Compensation: $138k - $165k + annual bonus + equity

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.

## Responsibilities

- Production pipeline development: Develop, test, and maintain NGS workflows for FASTQ processing, alignment, variant calling, annotation, QC reporting, and sample-level traceability.
- Assay translation: Partner with assay development and lab operations to move workflow changes from development into production without losing version control, auditability, or reproducibility.
- Regulatory validation support: 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, 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.
- Familiarity with 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 clinical reporting edge cases.
- Clear communication style for working with laboratory, QA, regulatory, and assay development stakeholders.

## Technical stack

Python, Bash, Nextflow/WDL/Snakemake, Docker, AWS, BWA/GATK/samtools, Picard/FastQC/MultiQC, VCF/BAM/FASTQ, CAP/CLIA documentation.