Bioinformatics Pipeline Engineer (Remote-US)

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