Remote: Lead Bioinformatics Pipeline Architect

Embedded Shishya; United States; Remote; USD 131,000 - 164,000; Full time

Job summary

Natera is seeking a Lead Bioinformatics Engineer to own pipeline and infrastructure engineering for a research informatics team working on cfDNA in Women's and organ health. This is an individual contributor role.

You will own WDL workflows, transition toward Nextflow, and manage the AWS infrastructure and tooling. You will inherit a working system and teach new approaches while driving cost and runtime improvements.

Qualifications

• Degree in Bioinformatics, Computer Science, Computational Biology, or a related field. A degree is not required: equivalent depth built through work counts.
• 4+ years of software or pipeline engineering experience, preferably in life sciences, sequencing, or production-adjacent settings.
• Demonstrated ownership of a system end to end, including production operations.

Responsibilities

• Maintain and improve WDL workflows on AWS Batch and HealthOmics.
• Own AWS infrastructure managed as code with Terraform; improve reliability and observability.
• Build and harden internal tooling to reduce manual work and improve testability.
• Use coding agents as part of engineering, review agent-written code to standards.
• Collaborate with science leads and data scientists to deploy methods into production pipelines.

Skills

Python

Workflow systems

Cloud infrastructure

Terraform

Linux / Containers

AI-assisted workflows

Learning agility

Documentation

Education

Degree in Bioinformatics or related field

Tools

AWS Batch

HealthOmics

Nextflow

WDL

Snakemake / CWL

Job description

Natera is seeking a Lead Bioinformatics Engineer to own pipeline and infrastructure engineering for a research informatics team working on cfDNA in Women's and organ health. This is an individual contributor role.

You will own WDL workflows, transition toward Nextflow, and manage the AWS infrastructure and tooling. You will inherit a working system and teach new approaches while driving cost and runtime improvements.