Genomic Diagnostics Software Engineer II

Children's Hospital of Philadelphia; Philadelphia (Philadelphia County); Hybrid; USD 101,000 - 129,000; Full time

Job summary

Children’s Hospital of Philadelphia (CHOP) is seeking a Software Engineer II to join the Genomic Diagnostic Laboratory's bioinformatics team. You will help develop and optimize pipelines and tools that support diagnostic testing and research while collaborating with lab directors, analysts and D&T services.

The role emphasizes Python development, HPC, UNIX/Linux environments, and data workflows, with opportunities to work on ETL, APIs, and cloud concepts.

Qualifications

• Bachelor's degree required in a computational discipline or related field.
• 3+ years in production, clinical or research bioinformatics data experience.
• 4+ years experience preferred in bioinformatics data processing.
• Extensive knowledge of high performance/parallel computing environments.
• Experience with HPC systems, job management and benchmarking.

Responsibilities

• Develop and optimize local large-scale bioinformatics pipelines.
• Manage HPC capability and data storage with IT and data center staff.
• Ensure availability and performance of bioinformatics software.
• Collaborate across stakeholders including lab management and D&T staff.
• Lead testing, deployment, and documentation of pipelines and tools.

Skills

Python development

Git

Unix/Linux

SQL

Full stack development

Ansible

HPC and job management (Slurm/qsub)

APIs (REST/GraphQL)

Workflow tools (Nextflow/Snakemake/CWL

RHEL OS

Education

Bachelor's Degree

Master's Degree in computational discipline or systems engineering

Tools

Git

Nextflow

Snakemake

CWL

WDL

REST API

GraphQL

Ansible

qsub/Slurm

Job description

Children’s Hospital of Philadelphia (CHOP) is seeking a Software Engineer II to join the Genomic Diagnostic Laboratory's bioinformatics team. You will help develop and optimize pipelines and tools that support diagnostic testing and research while collaborating with lab directors, analysts and D&T services.

The role emphasizes Python development, HPC, UNIX/Linux environments, and data workflows, with opportunities to work on ETL, APIs, and cloud concepts.