Senior Genomics Data Pipeline Engineer

myDNA, Inc.; Houston (TX); On-site; USD 140,000 - 190,000; Full time

Job summary

Gene by Gene seeks a Senior Data Pipeline Engineer/Developer to design, build, and own data pipelines moving genomic and operational data from lab instruments to analytics and clinical reporting. You will set technical direction for the data platform, ensure reproducible production pipelines, and guide engineering teams with architectural and code-level insights in a Python-first environment.

This 12-month contract focuses on data quality, lineage, observability, and strict regulatory

Qualifications

• Strong SQL proficiency on Microsoft SQL Server and PostgreSQL, including schema design and performance tuning.
• Strong Python proficiency across the stack; Python-first development.
• Experience with production workflow orchestrators (e.g., Argo Workflows, Airflow, Dagster, Prefect, Step Functions).
• Production experience with Docker and Kubernetes.
• Strong testing discipline across unit, integration, and data-quality tests.
• Excellent written and verbal communication for technical and compliance stakeholders.
• Genomics/NGS data formats handling (FASTQ, BAM/CRAM, VCF).
• Familiarity with bioinformatics workflow engines (Nextflow, WDL/Cromwell, Snakemake).
• AWS data stack expertise (S3, Glue, EMR, Redshift) and/or AWS HealthOmics.
• Distributed processing and streaming frameworks (Spark, Kafka, Kinesis).
• Data warehousing and transformation tooling (Snowflake, dbt).
• Infrastructure as code (Terraform, CDK, CloudFormation, Pulumi).
• LIMS integration and hybrid data architectures.

Responsibilities

• Builds and operates production ETL/ELT for high-volume genomic and operational data.
• Integrates data across LIMS, lab instruments, internal apps, and external sources.
• Develops across the stack in Python and provides guidance on data-layer integration.
• Sets technical direction for batch and streaming pipelines and leads adoption.
• Models and tunes data stores (SQL Server, PostgreSQL, cloud warehouse) for performance.
• Enforces testing, CI/CD, IaC, code reviews, and architecture decision records.
• Owns data quality, lineage, observability, and SLAs.
• Builds pipelines with versioned data and code for reproducibility and auditability.
• Collaborates with security/compliance on PHI/PII handling and regulatory requirements.
• Adheres to data-governance controls and least-privilege access across regions.

Skills

SQL

Python

Orchestration

Docker

Kubernetes

Testing

Communication

Genomics data

Bioinformatics

AWS

Spark

Snowflake

dbt

IaC

LIMS

C# / C++

Education

Bachelor's degree in Computer Science, Bioinformatics, or related field

Advanced degree preferred

Tools

Argo Workflows

Airflow

Dagster

Prefect

Step Functions

Docker

Kubernetes

Snowflake

dbt

Terraform

CloudFormation

Pulumi

Nextflow

WDL/Cromwell

Snakemake

Job description

Gene by Gene seeks a Senior Data Pipeline Engineer/Developer to design, build, and own data pipelines moving genomic and operational data from lab instruments to analytics and clinical reporting. You will set technical direction for the data platform, ensure reproducible production pipelines, and guide engineering teams with architectural and code-level insights in a Python-first environment.

This 12-month contract focuses on data quality, lineage, observability, and strict regulatory