Bioinformatics Pipeline Engineer, Remote – Must be based in the United States

Job Title: Bioinformatics Pipeline Engineer
Domain: Healthcare / Genomics
Location: Remote – Must be based in the United States
Contract Duration: 6 months

Job Overview
We are looking for a Bioinformatics Pipeline Engineer to develop, maintain, and improve software pipelines used to analyze genetic and genomic sequencing data.
The candidate will work with bioinformatics tools, cloud technologies, and programming languages to support genomic testing, variant analysis, data quality checks, and clinical reporting.
The role involves collaborating with software developers, research scientists, and clinical teams to build reliable and accurate solutions in a regulated healthcare environment.

Key Responsibilities

• Develop and maintain bioinformatics pipelines for Next-Generation Sequencing (NGS) data analysis.
• Analyze genomic sequencing data and support genetic variant analysis.
• Develop, test, validate, and implement software applications and data workflows.
• Use cloud platforms and container technologies to run and manage pipelines.
• Troubleshoot pipeline issues and provide technical support.
• Perform data quality checks and prepare technical reports.
• Work with software developers, research scientists, and clinical teams.
• Document workflows, testing procedures, and technical changes.
• Follow quality standards and controlled processes used in clinical diagnostics.

Required Skills

• Bioinformatics: Knowledge of genomic sequencing data analysis and variant analysis.
• Programming: Strong Python scripting skills.
• Workflow Management: Experience with Nextflow or similar pipeline workflow tools.
• Cloud: Experience with AWS.
• Containers: Experience with Docker.
• Version Control: Experience with Git.
• NGS Tools: Familiarity with tools such as BWA, FastQC, samtools, or VEP.
• Experience: Relevant experience working with biological, clinical, or genomic data.

Preferred Skills

• Experience with Nextflow, Cromwell, or CWL.
• Familiarity with DRAGEN, MultiQC, and bedtools.
• Experience with Terraform or AWS CDK.
• Knowledge of REST APIs and JSON.
• Experience with CI/CD tools, especially GitHub Actions.
• Familiarity with R, JavaScript/TypeScript, Flask, and data visualization tools.
• Experience with Jupyter Notebook or R Markdown.
• Familiarity with AI coding assistants such as GitHub Copilot.
• Experience in a clinical diagnostics laboratory or a regulated healthcare environment, such as CAP/CLIA.

Education and Experience

• Bachelor's degree with 3+ years of relevant experience, or
• Master's degree with 1+ year of relevant experience.

Candidates should have experience in bioinformatics, biological or clinical data, software development, or related technologies.