Bioinformatics Software Engineer NGS / Clinical Diagnostics at Secaucus, NJ (Remote)

Bioinformatics Software Engineer NGS / Clinical Diagnostics

Secaucus, NJ (Remote)

Long Term Contract

Mandatory Skills: Next-generation sequencing (NGS) data analysis, advanced diagnostic testing development ,database development, programming languages, cloud development, bioinformatic methods

Job Details:

• This position is in our Bioinformatics Solutions Engineering group, part of the Research and Development organization, in 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, develop, document, validation and launching of new high quality diagnostic tests and services for the benefit of our 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, and clinical reporting.
• Serve as SME on specific systems/workflows supporting advanced development and high-tier production support.
• Participate in resolution of 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 other Software Developers, R&D bench scientists, Genetic Counselors, Operations Scientists, and other technical business partners.

Qualifications:

• 3+ years of experience with a Bachelor's degree or 1+ year with a Master's degree and experience in an industrial or academic setting working with clinical and biological data or equivalent and underlying technologies including bioinformatic methods, database development, query/scripting/programming languages, cloud development, agile methodology, DevOps and other data analysis tools.
• Bioinformatics tools such as Dragen, bwa, VEP, FastQC, MultiQC, samtools, bedtools.
• Experience with sequencing data analysis, bioinformatics, variant data analysis.
• Pipeline workflow management languages: 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.
• Containerizing: Docker.
• Experience with designing and working with application programming interfaces (e.g. JSON based RESTful APIs).
• Web Frameworks: Python Flask, React Native, Bootstrap.
• Reporting: Familiarity with R Markdown, Jupyter Notebook.
• Visualization: Experience with any ggplot2/tidyverse, Plotly, matplot lib, Tableau, d3.js.
• Source Control: Git.
• CI/CD: GitHub CI/CD.
• Familiarity with AI developer tools like GitHub Copilot.
• Understanding of environment management.
• Experience of working in clinical diagnostics setting (regulations, controlled processes, environment management) is a plus.