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Bioinformatics Wdl Jobs (NOW HIRING)

Natera

Director of Data Science and Bioinformatics

OR · On-site +1

In this role, you will build the bioinformatics capability within the Data Science development team ... Experience with MLOps frameworks and pipeline tools (MLflow, Nextflow, WDL, Docker). * Advanced ...

Axle

Bioinformatics Scientist

Bethesda, MD · On-site

Bioinformatics Scientist To be considered for this position, please upload a document as your Cover ... Snakemake, Nextflow, CWL/WDL * Expertise building technical and user documentation for tools ...

Caris MPI, Inc.

Scientist - Bioinformatics

Phoenix, AZ · On-site

... as WDL or Nextflow is preferred.Skills in statistical analysis and data visualization with ... bioinformatics to build and maintain large scale pipelines.Physical DemandsMust possess ability to ...

Axle

Bioinformatics Scientist

Bethesda, MD · On-site

Bioinformatics Scientist To be considered for this position, please upload a document as your Cover ... Snakemake, Nextflow, CWL/WDL * Expertise building technical and user documentation for tools ...

Theiagen Genomics

Bioinformatics Analyst II

Denver, CO · On-site +1

$90K - $105K/yr

Advanced experience with cloud-based bioinformatics platforms (e.g., Terra.bio, Galaxy) and workflow orchestration tools (e.g., Nextflow, WDL, or Snakemake). * Hands-on expertise in using ...

Theiagen Genomics

Bioinformatics Analyst II

Denver, CO · On-site +1

$90K - $105K/yr

Advanced experience with cloud-based bioinformatics platforms (e.g., Terra.bio, Galaxy) and workflow orchestration tools (e.g., Nextflow, WDL, or Snakemake). * Hands-on expertise in using ...

New

Theiagen Genomics

Bioinformatics Analyst III

Denver, CO · Remote

Experience with bioinformatics tools, databases, and workflow management systems (Nextflow, Snakemake, WDL). * Demonstrated expertise applying bioinformatics tools and workflows to answer complex ...

New

Natera

Director of Data Science and Bioinformatics

$186K - $232K/yr

Build and define the Bioinformatics function within the Data Science development team, identify ... Experience with MLOps frameworks and pipeline tools (MLflow, Nextflow, WDL, Docker). * Advanced ...

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Bioinformatics Wdl information

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$59.5K

$94.5K

$149.5K

How much do bioinformatics wdl jobs pay per year?

As of Sep 12, 2026, the average yearly pay for bioinformatics wdl in the United States is $94,474.00, according to ZipRecruiter salary data. Most workers in this role earn between $67,500.00 and $129,500.00 per year, depending on experience, location, and employer.

What is a bioinformatics WDL?

A Bioinformatics WDL refers to the use of the Workflow Description Language (WDL) in bioinformatics to describe data analysis workflows. WDL is a specialized language designed to make it easier to write, share, and execute scientific workflows, particularly in genomics and other biological research. Bioinformatics professionals use WDL to automate complex analyses, ensuring reproducibility and scalability across different computing environments. Typical tasks include processing sequencing data, variant calling, and integrating results from various tools. Using WDL helps standardize bioinformatics pipelines and supports collaboration between researchers.

What are the key skills and qualifications needed to thrive as a bioinformatics WDL specialist?

To thrive as a Bioinformatics WDL specialist, you need a solid background in bioinformatics, scripting languages (such as Python or Bash), and experience with WDL for workflow development, typically supported by a relevant degree. Familiarity with workflow management systems like Cromwell, cloud platforms (e.g., Google Cloud or AWS), and version control tools (like Git) is commonly required. Strong problem-solving skills, attention to detail, and effective communication are essential soft skills for translating complex biological problems into reproducible computational workflows. These skills and qualities are crucial for ensuring robust, scalable, and reproducible analysis pipelines in collaborative research and clinical environments.

How does a bioinformatics WDL specialist typically collaborate with biologists and software engineers during project development?

Bioinformatics WDL specialists play a crucial role as liaisons between biologists, who define the scientific objectives, and software engineers, who optimize computational processes. They translate biological workflows into reproducible, automated pipelines using Workflow Description Language (WDL), ensuring computational tasks are scalable and robust. Regular meetings and clear documentation are essential, as specialists often gather biological requirements, design workflows, and coordinate with engineers to deploy them on cloud or HPC environments. This collaborative approach ensures that scientific goals are met efficiently and that pipelines are maintainable and reproducible.

What is the difference between Bioinformatics Wdl vs Bioinformatics Analyst?

AspectBioinformatics WdlBioinformatics Analyst
Required CredentialsBachelor's/Master's in Bioinformatics, Computer Science, or related field; familiarity with WdlBachelor's/Master's in Bioinformatics, Biology, or related field; experience with data analysis
Work EnvironmentResearch labs, biotech companies, or academic institutions using workflow managementData analysis teams, research institutions, healthcare organizations
Employer & Industry UsagePrimarily in genomics, biotech, and research projects involving workflow automationInvolved in interpreting biological data, reporting, and supporting research decisions

While Bioinformatics Wdl focuses on developing and managing bioinformatics workflows using Wdl, Bioinformatics Analysts primarily analyze biological data and interpret results. Both roles require strong bioinformatics skills, but Wdl specialists emphasize workflow automation, whereas analysts focus on data interpretation and reporting.

What other helpful pages are available for Bioinformatics Wdl?

Other pages related to Bioinformatics Wdl:

Infographic showing various Bioinformatics Wdl job openings in the United States as of September 2026, with employment types broken down into 86% Full Time, 12% Part Time, and 2% Contract. Highlights an 75% Physical, 4% Hybrid, and 21% Remote job distribution, with an average salary of $94,474 per year, or $45.4 per hour.

Software Engineer - Bioinformatics /NGS Sequencing Systems

South San Francisco, CA • On-site

APN Software Services Inc
IT Services • 51 - 200 employees
Learn more about APN Software Services Incexternal

Contractor

Re-posted 5 days ago

Job description

Job title: Bioinformatics Software Engineer – NGS Sequencing Systems
Duration: till end of year

Location: South SFO, CA

Position Summary
We are seeking a highly motivated Bioinformatics Software Engineer to support software systems and data workflows within a Next Generation Sequencing (NGS) laboratory environment. The successful candidate will develop, maintain, and support applications and pipelines used for sequencing data processing, laboratory workflow management, and data analysis.
This role requires a strong background in software development, database management, and workflow automation, with experience supporting scientific data systems. The candidate will collaborate closely with bioinformaticians, scientists, and laboratory staff to ensure reliable data processing and scalable analysis pipelines.
Experience with NGS sequencing workflows and bioinformatics tools is highly desirable, but not required.
Key Responsibilities
Software Development
● Design, develop, test, and maintain Java and Java EE web applications used to support sequencing lab workflows and laboratory data systems.
● Develop software tools to support sequencing data processing, data tracking, and laboratory operations.
● Participate in software design discussions and contribute to scalable and maintainable system architecture.
Workflow & Pipeline Development
● Develop and maintain bioinformatics pipelines for processing NGS data.
● Implement workflow automation using WDL (Workflow Description Language).
● Manage and support workflow execution through the Cromwell workflow engine.
● Optimize pipeline performance and ensure efficient processing of large sequencing datasets.
Database & Data Management
● Develop and execute SQL and PL/SQL queries to support data retrieval, transformation, and system integration.
● Support Oracle database systems, including writing queries, performing updates, and maintaining database integrity.
● Ensure reliable data storage, accessibility, and traceability across sequencing workflows.
Data Processing & Automation
● Develop and maintain Python and Bash scripts to automate data processing, analysis workflows, and system integration tasks.
● Implement data validation and quality checks to ensure accuracy and consistency of sequencing data.
Systems Integration
● Integrate laboratory information systems such as LIMS with sequencing platforms and downstream analysis pipelines.
● Support data flow between laboratory instruments, analysis systems, and databases.
Infrastructure & Deployment
● Support deployment and execution of pipelines in High Performance Computing (HPC) environments.
● Assist with cloud-based workflow deployment using AWS services.
● Build and maintain containerized software environments (e.g., Docker) to ensure reproducibility of computational workflows.
Troubleshooting & Support
● Monitor and troubleshoot pipeline execution issues and system performance problems.
● Identify and resolve bottlenecks in data processing pipelines.
● Provide technical support to scientists and lab personnel using the software systems.
Collaboration
● Work closely with bioinformaticians, data scientists, software engineers, and laboratory staff to understand workflow requirements.
● Translate scientific and operational needs into scalable software solutions.
● Participate in cross-functional discussions to improve sequencing workflow efficiency.
Documentation & Best Practices
● Maintain clear documentation of pipelines, applications, and database structures.
● Use Git repositories and version control best practices to manage software development.
● Support testing, validation, and continuous improvement of systems.
Required Qualifications
● Bachelor’s or Master’s degree in Computer Science, Bioinformatics, Computational Biology, Software Engineering, or related field w/ MIN 3 years exp
● Strong experience with Oracle databases.
● Proficiency in SQL and PL/SQL.
● Experience with Java and Java EE web application development.
● Strong programming skills in Python.
● Experience with Bash scripting.
● Experience developing or supporting workflow pipelines using WDL.
● Familiarity with the Cromwell execution framework.
● Experience working with data processing pipelines or scientific data systems.
Preferred Qualifications
● Experience working in NGS sequencing or genomics environments.
● Familiarity with bioinformatics data processing workflows.
● Experience working in HPC computing environments.
● Experience with AWS cloud services.
● Experience with container technologies (Docker, Singularity, etc.).
● Experience using Git version control systems.
● Experience supporting LIMS systems or laboratory data platforms.
Skills & Competencies
● Strong problem-solving and troubleshooting skills.
● Ability to work independently in a fast-paced research environment.
● Strong communication skills and ability to collaborate with scientific teams.
● Ability to manage multiple priorities and support complex data workflows.
Interview process: 1. phone (15-20mins) 2. In-person (1 hr)
Hybrid- 2-3 days onsite
Function: gRED


APN Software services Inc. is an equal opportunity employer. All applicants will be considered for employment without attention to race, color, religion, sex, sexual orientation, gender identity, national origin, veteran or disability status.”