About the role
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