Remote Genomics Software Engineer — Pipelines & Tools

Singular Genomics; San Diego (CA); Hybrid; USD 108,000 - 128,000; Full time

Job summary

Singular Genomics is seeking a Software Engineer to join our core software team, contributing across pipeline engineering, tooling, and field support. You will work on our sequencing analysis platform, fixing bugs, improving validation logic, and maintaining build and regression infrastructure.

The role emphasizes solid Python fundamentals and comfort across a large production codebase. This position can be remote or on-site, with quarterly travel to our San Diego HQ as needed.

Qualifications

• 2–5 years of professional software engineering experience.
• Solid Python skills; comfortable working in a large, production codebase with real operational requirements.
• Familiarity with Linux, HPC environments, and distributed job execution.
• Experience with build systems, CI/CD pipelines, and package tooling (e.g., Jenkins, Bitbucket, Poetry).
• Comfortable reading and debugging across a broad codebase, including relational databases, web services and pipeline orchestration (Airflow or similar).
• Working knowledge of JavaScript and openness to learning TypeScript.
• Strong debugging instincts and the ability to triage ambiguous failures under time pressure.
• Good communication and collaboration skills in a team environment.

Responsibilities

• Contribute to active development on the sequencing analysis pipeline in Python, including bug fixes, feature work, and code reviews.
• Own and maintain build configuration, CI/CD pipelines, and regression infrastructure (Jenkins, Bitbucket, HPC).
• Respond to inbound triage requests from the field and internal teams, diagnosing and resolving pipeline failures on sequencing instruments.
• Develop and maintain operational tooling including re-run utilities, job monitoring, and pipeline configuration management.
• Work on data handling features including backup/upload logic, panel management, and sample sheet validation.
• Implement locking, concurrency controls, and other reliability improvements to the pipeline execution framework.
• Support package management and dependency maintenance across Python and JavaScript/TypeScript projects.
• Develop and maintain lightweight web services, internal APIs, and database-backed tooling to support engineering and field operations.
• Identify and close gaps in observability, documentation, and operational processes.

Skills

Python

Linux

HPC

CI/CD

Debugging

Communication

Collaboration

TypeScript

Airflow

Tools

Jenkins

Bitbucket

Poetry

Airflow

Flask

Django

Docker

PostgreSQL

Job description

Singular Genomics is seeking a Software Engineer to join our core software team, contributing across pipeline engineering, tooling, and field support. You will work on our sequencing analysis platform, fixing bugs, improving validation logic, and maintaining build and regression infrastructure.

The role emphasizes solid Python fundamentals and comfort across a large production codebase. This position can be remote or on-site, with quarterly travel to our San Diego HQ as needed.