onsite
Bioinformatics Engineer - SurveillanceBench - LatchBio
Research Engineer
Lead the design and execution of scalable bioinformatics pipelines for pathogen surveillance, leveraging Python, Nextflow, and Docker on AWS to process wastewater and environmental metagenomic data for outbreak detection.
About the role
Key Responsibilities
- Design, develop, and maintain reproducible computational workflows for wastewater sequencing, air sampling, and metagenomic analysis using Nextflow and Snakemake.
- Implement containerized pipelines with Docker and deploy them on AWS infrastructure for scalable, high‑throughput processing.
- Collaborate with data scientists to create benchmark datasets and evaluation metrics for AI models in infectious disease surveillance.
- Optimize performance and resource usage, ensuring rapid turnaround for outbreak detection and public health response.
- Document pipeline architecture, usage guidelines, and best practices for internal and external stakeholders.
Requirements
- Strong programming skills in Python and experience with workflow managers (Nextflow/Snakemake).
- Hands‑on experience in molecular epidemiology, wastewater genomics, and environmental metagenomics.
- Proficiency in Docker containerization and cloud deployment (AWS).
- Excellent problem‑solving abilities and a passion for open‑source bioinformatics tools.
- Effective communication skills for cross‑functional collaboration.