Bioinformatics Pipeline Engineer (Remote-US)

OMG Technology; Jersey City (NJ); Remote; USD 110,000 - 165,000; Full time

Job summary

OMG Technology is seeking a Bioinformatics Pipeline Engineer for a 6+ month remote contract in the United States. You will work in a regulated CAP/CLIA lab environment on end-to-end design, validation, and deployment of diagnostic test software for NGS data analysis.

The role involves collaboration with software developers, bench scientists, and other technical partners. Strong Python/JavaScript/R skills, cloud and DevOps experience, and familiarity with Nextflow are desired.

Qualifications

• 5+ years with a Bachelor's degree or 2+ years with a Master’s degree in clinical/biological data.
• Experience with bioinformatics tools, data analysis, and sequencing data analysis.
• Familiarity with cloud development and DevOps practices.
• Experience in a regulated clinical diagnostics setting is a plus.

Responsibilities

• Develop, validate, and implement software for NGS data analysis and clinical reporting.
• Serve as SME for systems/workflows in advanced development and production support.
• Provide data analyses and regular progress reports for internal review.
• Prepare communications of technical activities aligned with business objectives.
• Collaborate with software developers, scientists, and operations teams on projects.

Skills

Python

JavaScript/TypeScript

R

Bioinformatics methods

NGS data analysis

Data analysis

Clinical data

Education

Bachelor's degree

Master's degree

Tools

Nextflow

Cromwell

CWL

Docker

AWS

Terraform

Git

GitHub CI/CD

Job description

Bioinformatics Pipeline Engineer

We are looking to hire a candidate with the mentioned skill sets and experience for one of our clients. This is a 6+ month contracting role, with potential for extension. This is a REMOTE role. This position can be 100% remote and the candidate must be located in the United States.

Overview As a Bioinformatics Engineer, you will work for the industry leader, with a career where you can collaborate and affect change while expanding your leadership skills and technical knowledge. You can make a real impact in a growing and developing market.

This position is in our Bioinformatics Solutions Engineering group, part of the Research and Development organization, in the Molecular Genomics & Oncology unit. The team supports genetic/genomic testing in a highly regulated CAP/CLIA laboratory environment, primarily using short- and long-read sequencing as the basis of evidence.

The right candidate will know how to balance innovation, standards, and quality with a practical understanding of when each is appropriate. The Bioinformatics Solutions Engineering group is a cross-functional unit focusing on end-to-end design, development, documentation, validation, and launching of new high-quality diagnostic tests and services for patients.

Responsibilities

• Develop, validate, and implement new software applications, databases, processes, and interfaces relating to: Next-generation sequencing (NGS) data analysis, Advanced diagnostic testing development and validation, Data quality review, Clinical reporting
• Serve as an SME on specific systems/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 of technical activities related to business objectives, such as product/process development and improvement.
• Activities may be focused individual projects or, more usually, assignments as a member of a project team, often working closely with: Software Developers, R&D bench scientists, Genetic Counselors, Operations Scientists, Other technical business partners

Qualifications

• 5+ years of experience with a Bachelor’s degree or 2+ year of experience with a Master’s degree, in an industrial or academic setting working with clinical and biological data or equivalent.
• Experience with underlying technologies including Bioinformatic methods, Database development, query/scripting/programming languages, Cloud developmen, Agile methodology, DevOps and other data analysis tools

Required skills:

• Bioinformatics Tools: DRAGEN, BWA, VEP, FastQC, MultiQC, samtools, bedtools
• Sequencing & Bioinformatics: Experience with sequencing data analysis, bioinformatics, and variant data analysis
• Pipeline Workflow Management: Nextflow (preferred), Cromwell, CWL, etc.
• Cloud Computing: AWS
• Infrastructure Management: Terraform, AWS CDK
• Programming Languages: Advanced level with interpreted/scripting languages such as Python, JavaScript/TypeScript, R, etc.
• Containerization: Docker
• APIs: Experience designing and working with application programming interfaces, such as JSON-based RESTful APIs
• Web Frameworks: Python Flask, React Native, Bootstrap
• Reporting: Familiarity with R Markdown and Jupyter Notebook
• Visualization: Experience with any of ggplot2/tidyverse, Plotly, matplotlib, Tableau, or d3.js
• Source Control: Git
• CI/CD: GitHub CI/CD
• AI Developer Tools: Familiarity with tools such as GitHub Copilot
• Environment Management: Understanding of environment management
• Clinical Diagnostics: Experience working in a clinical diagnostics setting, including regulations, controlled processes and environment management, is a plus

Other Job Details:

• Location: REMOTE
• Duration: 6 - 12 months
• Docs required: ID proof will be required