Senior Genomics Data Pipeline Architect

Gene by Gene; Houston (TX); On-site; USD 140,000 - 180,000; Full time

Job summary

Gene by Gene seeks a Senior Data Pipeline Engineer/Developer to design, build, and own data pipelines that move genomic and operational data from lab instruments through analytics and clinical reporting. This Python-first, contractor role sets technical direction for the data platform and ensures reproducibility and auditability in a regulated environment.

You will own data quality, lineage, observability, and guide engineering teams on data-layer integration while enforcing CI/CD and security

Qualifications

• Strong SQL proficiency on MS SQL Server and PostgreSQL, including schema design and tuning.
• Strong Python proficiency across the stack (data pipelines, back-end services, APIs).
• Production experience with a workflow orchestrator (Argo, Airflow, Prefect, Dagster, etc.).
• Production experience with containers (Docker) and Kubernetes for orchestration.
• Strong testing discipline: unit, integration, and data‑quality tests.
• Excellent written and verbal communication for technical and compliance stakeholders.
• Genomics/NGS data formats (FASTQ, BAM/CRAM, VCF).
• Bioinformatics workflow engines (Nextflow, WDL/Cromwell, Snakemake).
• AWS data stack (S3, Glue, EMR, Redshift) and/or AWS HealthOmics.
• Distributed processing/streaming (Spark, Kafka, Kinesis).
• Data warehousing/transformation tools (Snowflake, dbt).
• Infrastructure as code (Terraform, CDK, CloudFormation, Pulumi).
• Familiarity with .NET/C++ for integrating with existing services.
• LIMS integration and hybrid data architectures.

Responsibilities

• Builds and operates production ETL/ELT for genomic and operational data.
• Integrates data across LIMS, lab instruments, internal apps and third-party sources.
• Develops Python data services and internal APIs; guides data-layer integration.
• Sets technical direction for batch and streaming pipelines; evaluates frameworks and storage patterns.
• Models data stores (SQL Server, PostgreSQL, cloud warehouse) for performance and scale.
• Enforces testing, CI/CD, infrastructure as code, and architecture decision records.
• Owns data quality, lineage, observability, freshness, schema drift, and SLAs.
• Partners with security/compliance on PHI handling and regulatory requirements.

Skills

SQL proficiency

Python proficiency

Workflow orchestration

Docker

Kubernetes

Testing discipline

Communication skills

Genomics data

Bioinformatics workflows

AWS data stack

Big data frameworks

dbt

IaC

LIMS integration

Education

Bachelor's in CS/Bioinformatics

Advanced degree preferred

Tools

Argo Workflows

Step Functions

Prefect

Dagster

Airflow

Spark

Kafka

Kinesis

Snowflake

dbt

Terraform

CDK

CloudFormation

Pulumi

Job description

Gene by Gene seeks a Senior Data Pipeline Engineer/Developer to design, build, and own data pipelines that move genomic and operational data from lab instruments through analytics and clinical reporting. This Python-first, contractor role sets technical direction for the data platform and ensures reproducibility and auditability in a regulated environment.

You will own data quality, lineage, observability, and guide engineering teams on data-layer integration while enforcing CI/CD and security