Bioinformatics Software Engineer

We are seeking a
Bioinformatics Software Engineer
to support software systems and data workflows in a
Next Generation Sequencing (NGS) laboratory environment
. This role focuses on developing and maintaining bioinformatics pipelines, supporting sequencing data processing, and building scalable tools for laboratory workflow automation and data analysis.

The ideal candidate will collaborate with
bioinformaticians, scientists, and software engineers
to ensure reliable data processing and efficient analysis pipelines for genomics research.

This role requires strong programming skills and experience working with
bioinformatics pipelines, sequencing data systems, and workflow automation technologies
.

Key Responsibilities

- Design and develop
Java and Java EE applications
supporting sequencing lab workflows and data systems
- Build and maintain
bioinformatics pipelines for NGS data processing
- Develop
Python and Bash scripts
for workflow automation and data processing
- Implement workflow orchestration using
WDL and Cromwell
- Develop
SQL and PL/SQL queries
to support data retrieval and integration with Oracle databases
- Integrate
LIMS systems and sequencing platforms
with downstream analysis pipelines
- Support pipeline execution in
HPC and cloud environments
- Build containerized environments using
Docker
to ensure reproducible workflows
- Troubleshoot pipeline performance issues and optimize processing of large datasets
- Collaborate with scientists and engineering teams to improve sequencing workflow efficiency

Basic Qualifications

- Bachelor’s or Master’s degree in
Computer Science, Bioinformatics, Computational Biology, or related field
- 3+ years of experience
working with bioinformatics pipelines or scientific data systems
- Experience with
Java / Java EE development
- Strong programming skills in
Python
- Experience with
SQL / PL-SQL and Oracle databases
- Experience with
Bash scripting
- Experience with
WDL workflows and Cromwell execution engine

Preferred Qualifications

- Experience working with
NGS sequencing or genomics pipelines
- Experience in
HPC computing environments
- Familiarity with
AWS cloud services
- Experience with
Docker or containerized workflows
- Experience supporting
LIMS systems
- Experience using
Git version control