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, build production pipelines at scale, and provide guidance to engineering teams on data-layer integration in a Python-first environment.

Qualifications

• Strong SQL proficiency on Microsoft SQL Server and PostgreSQL, including schema design, query tuning, and performance troubleshooting.
• Strong Python proficiency across the stack (data pipelines, backend services, and APIs). This is a Python-first role.
• Production experience with a workflow orchestrator (Argo Workflows, Step Functions, Prefect, Dagster, Airflow, or similar).
• Production experience with containers (Docker) and Kubernetes, which the lead orchestrator (Argo Workflows) runs on.
• Strong testing discipline, including unit, integration, and data-quality or contract tests.
• Excellent written and verbal communication, including the ability to explain data tradeoffs to technical and compliance stakeholders.
• Genomics or NGS data formats and handling (FASTQ, BAM/CRAM, VCF).
• Bioinformatics workflow engines (Nextflow, WDL/Cromwell, or Snakemake).
• AWS data stack proficiency (S3, Glue, EMR, Batch, Lambda, Redshift) and/or AWS HealthOmics.
• Distributed processing and streaming frameworks (Spark, Kafka, Kinesis).
• Data warehouse and transformation tooling (Snowflake, dbt).
• Infrastructure as code practices (Terraform, CDK, CloudFormation, or Pulumi).
• Familiarity with .NET (C#) and/or C++ as supporting languages for integrating with existing services.
• Knowledge of LIMS integration and on-premises plus hybrid data architectures.

Responsibilities

• Builds and operates production ETL and ELT for high-volume genomic data as well as operational and business data.
• Integrates data across LIMS, lab instruments, internal applications, and third-party sources through robust, well-tested interfaces.
• Develops across the stack in Python (data services, internal APIs, and supporting application code) and provides architectural and code-level guidance to engineering teams on data-layer integration.
• Architecture & Technical Leadership: Sets technical direction for batch and streaming data pipelines by evaluating frameworks, orchestration, storage, and processing patterns.
• Models and tunes data stores (Microsoft SQL Server and PostgreSQL, plus a cloud warehouse or lake) for performance and scale.
• Defines and enforces engineering standards for testing, CI/CD, infrastructure as code, code review, and architecture decision records.
• Data Quality & Pipeline Observability: Owns data quality, lineage, and observability, including freshness, completeness, schema-drift detection, cost-per-job, and SLAs.

Skills

SQL proficiency

Python proficiency

Workflow orchestration

Docker & Kubernetes

Testing discipline

Communication with stakeholders

Genomics data handling

Education

Bachelor's degree in CS or related field

Advanced degree preferred

Tools

Argo Workflows

Airflow

Dagster

Kubernetes

Docker

dbt

Snowflake

AWS data stack (S3/Redshift)

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, build production pipelines at scale, and provide guidance to engineering teams on data-layer integration in a Python-first environment.