Bioinformatics Engineer II — NGS Data & Pipelines

Thornton Tomasetti; Madison (WI); Hybrid; USD 68,000 - 136,000; Full time

Job summary

Abbott Laboratories in Madison, WI is seeking a Bioinformatician II to support clinical reporting by monitoring variant calls and pipeline outputs. You will investigate QC issues, assist assay validation, and contribute to regulatory inspections while handling data management and customer deliveries.

The role emphasizes multi-language programming, tool development, and collaboration across teams, with an on-site schedule Tue–Sat and opportunities to mentor junior staff.

Qualifications

• Bachelor’s or Master’s degree in Bioinformatics/CS/Computational Biology or related field.
• 2 years of job-related experience in biomedical data analysis.
• Proficiency in Python and Java and building workflows.
• Proficiency with Linux/UNIX and shell scripting.
• Experience with MATLAB/R for data analysis and statistics.
• Familiarity with NGS workflows and cloud computing.

Responsibilities

• Support clinical reporting by monitoring variant calls and pipeline outputs.
• Investigate quality control issues and participate in assay validation and regulatory inspections.
• Monitor bioinformatics NGS pipelines and data management for customers.
• Develop front ends for analysis tools and build automated workflows.
• Mentor junior staff and collaborate across teams to meet objectives.

Skills

Python

Java

Linux/UNIX

MATLAB/R

Version control

NGS workflows

AWS

Cromwell/WDL

Snakemake

HPC

Education

Bachelor’s or Master’s degree in Bioinformatics/CS/Computational Biology

Tools

Cromwell/WDL

Snakemake

DNAnexus

AWS

Job description

Abbott Laboratories in Madison, WI is seeking a Bioinformatician II to support clinical reporting by monitoring variant calls and pipeline outputs. You will investigate QC issues, assist assay validation, and contribute to regulatory inspections while handling data management and customer deliveries.

The role emphasizes multi-language programming, tool development, and collaboration across teams, with an on-site schedule Tue–Sat and opportunities to mentor junior staff.