Software Engineer – Bioinformatics Pipelines

Ontrac Solutions Llc; Chicago (IL); Remote; USD 120,000 - 160,000; Full time

Job summary

Ontrac Solutions Llc seeks a Software Engineer (Bioinformatics Pipelines) to join a 12–18 month program supporting a genomics unit in a healthcare customer. The role focuses on engineering pipelines, software quality, and automation, with remote work in the United States.

Ideal candidates have production experience with Python, Bash, and Nextflow, plus strong fundamentals in software engineering and experience in agile teams.

Qualifications

• Strong background in bioinformatics pipeline engineering and software quality.
• Proficiency in Python and Bash.
• Experience with Nextflow and HPC on-prem environments.
• Experience integrating pipelines with laboratory systems and sequencing instruments.
• Experience working in an agile team.

Responsibilities

• Maintain and improve the genomics pipelines running in the customer's on-premise HPC environment.
• Tune the performance of the pipelines in the HPC environment.
• Automate pipeline operations and recurring engineering tasks.
• Provide operational support for the pipelines, including troubleshooting failures and resolving issues in the movement and delivery of genomic data.
• Implement and maintain integrations between the pipelines and laboratory systems and sequencing instruments.
• Support the LIS transition work alongside Beaker as needed.
• Participate as a full member of an agile pipeline team for the duration of the engagement.

Skills

Bioinformatics pipelines

Python

Bash

Nextflow

HPC

Agile teamwork

Software engineering fundamentals

Lab systems integration

Tools

Nextflow

Python

Bash

Job description

OVERVIEW

OnTrac is seeking a highly skilled and experienced Software Engineer (Bioinformatics Pipelines) to join a contractor program supporting a critical customer engagement: the genomics unit of a healthcare customer, which requires a temporary software engineer on its pipeline teams for the next 12 to 18 months. The need is driven by a short-term increase in workload from an organization-wide transition of the Laboratory Information System (LIS) from Soft to Epic Beaker.

This role is ideal for a software engineer with a strong background in bioinformatics who can integrate into an established pipeline team quickly and begin contributing with limited ramp-up. It is not suited to a biologist with some programming skills; the work centers on the engineering of the pipelines (software quality, performance, automation, and operational support) rather than on scientific discovery. The successful candidate will work closely with the delivery team and customer stakeholders, including the customer's dedicated bioinformatics team, to ensure project success from initial definition through final delivery.

ENGAGEMENT

• Expected start date: 2 November 2026
• Duration: 12 to 18 months
• Location: United States only, fully remote

REQUIRED CREDENTIALS

• Professional software engineering experience with a demonstrated background in bioinformatics pipeline engineering
• Hands-on production experience with Python, Bash, and Nextflow

REQUIRED QUALIFICATIONS

• Strong software engineering fundamentals applied to bioinformatics pipelines, with a focus on software quality, performance tuning, automation, and operational support
• Proficiency in Python and Bash
• Experience with Nextflow for workflow management
• Experience developing, tuning, and operating pipelines in an on-premise high-performance computing (HPC) environment
• Experience integrating software with laboratory systems and sequencing instruments
• Experience working as a member of an agile team
• Ability to integrate into an established team quickly and contribute with limited ramp-up

USEFUL QUALIFICATIONS

• Direct experience with Illumina, Oxford Nanopore, or PacBio sequencing platforms

SCOPE AND DELIVERY EXPECTATIONS

The following covers the scope of work we anticipate the contractor supporting throughout the project. This scope is in line with our expectations of the project but is subject to change.

• Maintain and improve the software quality of the genomics pipelines running in the customer's on-premise HPC environment
• Tune the performance of the pipelines in the HPC environment
• Automate pipeline operations and recurring engineering tasks
• Provide operational support for the pipelines, including troubleshooting failures and resolving issues in the movement and delivery of genomic data
• Implement and maintain integrations between the pipelines and laboratory systems and sequencing instruments, including Illumina, Oxford Nanopore, and PacBio platforms
• Implement and maintain the technical infrastructure that enables the movement, analysis, and delivery of genomic data, working alongside the customer's bioinformatics team, which owns the biological aspects of the analyses
• Support the additional pipeline workload arising from the organization-wide LIS transition from Soft to Epic Beaker
• Participate as a full member of an agile pipeline team for the duration of the engagement