Bioinformatics Pipeline Engineer (Remote-US)

OMG Technology • Jersey City, NJ

1d • Remote

About The Position

This is a remote, 6+ month contract role with potential for extension. The candidate must be located in the United States. The position is part of the Bioinformatics Solutions Engineering group within Research and Development, in the Molecular Genomics & Oncology unit. The group supports genetic and genomic testing in a highly regulated CAP/CLIA laboratory environment, primarily using short- and long-read sequencing.

The Bioinformatics Pipeline Engineer will contribute to end-to-end design, development, documentation, validation, and launch of diagnostic tests and services. The role calls for balancing innovation, standards, and quality with practical judgment, and includes developing and supporting solutions for sequencing-data analysis, diagnostic testing, data quality review, and clinical reporting. Work may be on individual projects or as part of cross-functional teams.

Requirements

• At least 5 years of experience with a bachelor’s degree, or at least 2 years of experience with a master’s degree, in an industrial or academic setting working with clinical and biological data, or equivalent.
• Experience with bioinformatics methods, database development, query/scripting/programming languages, cloud development, Agile methodology, DevOps, and other data analysis tools.
• Experience with sequencing data analysis, bioinformatics, and variant data analysis.
• Advanced-level ability with interpreted or scripting languages such as Python, JavaScript/TypeScript, or R.
• Experience designing and working with application programming interfaces, such as JSON-based RESTful APIs.
• Experience with visualization tools such as ggplot2/tidyverse, Plotly, matplotlib, Tableau, or d3.js.
• Familiarity with R Markdown and Jupyter Notebook.
• Understanding of environment management.
• Familiarity with bioinformatics tools including DRAGEN, BWA, VEP, FastQC, MultiQC, samtools, and bedtools.
• Knowledge of pipeline workflow management tools such as Cromwell or CWL.

Nice To Haves

• Nextflow pipeline workflow management experience is preferred.
• Experience working in a clinical diagnostics setting, including regulations, controlled processes, and environment management, is a plus.
• Familiarity with GitHub Copilot or similar AI developer tools.

Responsibilities

• Develop, validate, and implement software applications, databases, processes, and interfaces for NGS data analysis, advanced diagnostic testing development and validation, data quality review, and clinical reporting.
• Serve as a subject matter expert for specific systems and workflows supporting advanced development and high-tier production support.
• Participate in resolving support requests.
• Regularly report progress and prepare data analyses for internal review.
• Prepare reports and other communications about technical activities related to business objectives, including product and process development and improvement.
• Work on individual projects or as a member of project teams, collaborating with software developers, R&D bench scientists, genetic counselors, operations scientists, and other technical business partners.

What This Job Offers

• Career Level: Mid Level