Software Engineer

Singular Genomics•San Diego, CA

11d•$108,400 - $127,500•Hybrid

About The Position

We're looking for a Software Engineer to join our core software team and contribute across pipeline engineering, operational tooling, and field support. This is a generalist role, where you will be embedded in the team that builds and maintains our core sequencing analysis platform, and you'll help keep that platform healthy and the team around it moving fast. On any given day, that might mean fixing a bug in the image backup pipeline, triaging a failed sequencing run reported by the field team, improving panel validation logic, or maintaining the build and regression infrastructure that the team depends on. You don't need deep expertise in any one niche, you need solid Python fundamentals, a get-things-done orientation, and the judgment to work confidently across a large, real production codebase. This position can be remote or on-site. If remote, travel to the headquarters in San Diego, CA will be required at least quarterly.

Requirements

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.

Nice To Haves

Familiarity with genomics, sequencing data, or scientific computing pipelines (Numpy, Scipy, RAPIDS, POLARS, etc).
Experience with PostGRES, celery and Flask.
Exposure to Django or similar Python web frameworks.
Experience with Docker and containerized workflows.
Familiarity with Airflow or other workflow orchestration systems.

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.