Software Engineer

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

ABOUT SINGULAR GENOMICS

Singular Genomics is inventing at the forefront of genomics, one of the world’s fastest-growing industries. The commercially available G4® Sequencing Platform is a powerful, highly versatile benchtop genomic sequencer designed to produce fast and accurate results. In addition, the company is currently developing the G4X™ Spatial Sequencer, an upgrade to the G4, which will leverage Singular’s proprietary sequencing technology, applying it as an in situ readout for transcriptomics, proteomics and fluorescent H&E in tissue, with spatial context. Singular Genomics’ mission is to empower researchers and clinicians to advance science and medicine.
We foster a culture of creativity and technical excellence, both catalysts for innovation. We celebrate diversity, emphasize collaboration and, as we rapidly mature, we are constantly looking at ways we can do better for our people.

Our Headquarters are located on the Torrey Pines Mesa, in La Jolla, California at the center of the biotech hub. Our Manufacturing facility is in Sorrento Valley.

Position Summary:

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.

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.

Required 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.

Preferred Qualifications:

• 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.

The estimated base salary range for this role based in the United States of America is: $108,400 - $127,500. Additionally, this role is eligible for to receive equity as part of the compensation package. Compensation decisions are dependent on several factors including, but not limited to, an individual’s qualifications, location where the role is to be performed, internal equity, and alignment with market data. Should the level of the role change during the hiring process, the applicable salary range may be updated accordingly.

Singular Genomics is an equal opportunity employer. We celebrate diversity and are committed to creating an inclusive environment for all employees. Singular Genomics is committed to working with and providing reasonable accommodations to job applicants with physical or mental disabilities. Applicants with a disability who require a reasonable accommodation for any part of the application or hiring process can provide their name and contact information to our Accommodations team at [e-mail]. Your request will be responded to as soon as possible.