Bioinformatics Workflow Developer

Zifo; Cary (NC); On-site; USD 100,000 - 160,000; Full time

Benefits offered by this job

Medical, dental, vision insurance

401k with company matching

Paid vacation

Life insurance

Flexible spending accounts

Job summary

Zifo is seeking a bioinformatics engineer to design, develop, and productionize scalable workflows for pangenome, haplotype, imputation, and QC, leveraging cloud-native AWS services. You will convert research scripts into automated, reproducible pipelines and collaborate with scientists to ensure biological accuracy of outputs.

Responsibilities include building robust pipelines, integrating validation and logging, and delivering reusable modules with documentation.

Qualifications

• Strong programming in Python, Nextflow, Snakemake, WDL, or similar workflow frameworks.
• Experience processing large-scale genomics datasets and common bioinformatics file formats.
• Familiarity with AWS cloud services and distributed computing.
• Understanding of software engineering best practices, including Git, testing, CI/CD, and documentation.

Responsibilities

• Design, develop, and productionize scalable bioinformatics workflows for pangenome, haplotype, imputation, and QC processes.
• Convert research scripts and manual analyses into automated, version-controlled, and reproducible pipelines.
• Work with genomic data formats including FASTA, GFF/GTF, VCF, BAM/CRAM, haplotype outputs, and associated metadata.
• Implement workflows using cloud-native AWS services, leveraging S3 storage and scalable batch execution.
• Build validation, logging, provenance tracking, and error-handling capabilities into workflows.
• Collaborate with scientists and domain experts to ensure biological accuracy and usability of outputs.

Skills

Python

Nextflow

Snakemake

WDL

CI/CD

Git

Documentation

Tools

AWS

Docker

Job description

Design, develop, and productionize scalable bioinformatics workflows supporting pangenome graph construction, haplotype expansion, population-scale imputation, and genomic data quality control. This role focuses on transforming research-grade analyses into robust, reusable, and cloud-enabled pipelines that support large-scale multi-crop genomics programs.

• Develop and maintain production-grade bioinformatics workflows for pangenome, haplotype, imputation, and QC processes.
• Convert research scripts and manual analyses into automated, version-controlled, and reproducible pipelines.
• Work with genomic data formats including FASTA, GFF/GTF, VCF, BAM/CRAM, haplotype outputs, and associated metadata.
• Implement workflows using cloud-native AWS services, leveraging S3 storage and scalable batch execution.
• Build validation, logging, provenance tracking, and error-handling capabilities into workflows.
• Collaborate with scientists and domain experts to ensure biological accuracy and usability of outputs.

Required Skills

• Strong programming experience in Python, Nextflow, Snakemake, WDL, or similar workflow frameworks.
• Experience processing large-scale genomics datasets and common bioinformatics file formats.
• Familiarity with AWS cloud services and distributed computing environments.
• Understanding of software engineering best practices, including Git, testing, CI/CD, and documentation.

Key Deliverables

• Production-ready workflow modules and reusable pipeline templates.
• Automated QC and validation reports.
• Execution and operational documentation.
• Reliable mechanisms for workflow monitoring, reprocessing, and onboarding of new datasets.

About Zifo:

CURIOSITY DRIVEN, SCIENCE FOCUSED, EMPLOYEE BUILT. Our culture is unlike any other, one where we debate, challenge ourselves, and interact with all alike. We are a curious bunch, characterized by our passion to learn and spirit of teamwork. Zifo is a global R&D solutions provider focused on the industries of Pharma, Biotech, Manufacturing QC, Medical Devices, specialty chemicals and other research-based organizations. Our team’s knowledge of science and expertise in technology help Zifo better serve our customers around the globe, including 7 of the Top 10 Biopharma companies.

We look for Science – Biotechnology, Pharmaceutical Technology, Biomedical Engineering, Microbiology etc. We possess scientific and technical knowledge and bear professional and personal goals. While we have a “no doors” policy to promote free access within, we do have a tough door to walk in. We search with a two-point agenda – technical competency and cultural adaptability.

We offer a competitive compensation package including accrued vacation, medical, dental, vision, 401k with company matching, life insurance, and flexible spending accounts.

If you share these sentiments and are prepared for the atypical, then Zifo is your calling!

Zifo is an equal opportunity employer, and we value diversity at our company. We do not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status.

CURIOSITY DRIVEN, SCIENCE FOCUSED, EMPLOYEE BUILT. Our culture is unlike any other, one where we debate, challenge ourselves, and interact with all alike. We are a curious bunch, characterized by our passion to learn and spirit of teamwork. Zifo is a global R&D solutions provider focused on the industries of Pharma, Biotech, Manufacturing QC, Medical Devices, specialty chemicals and other research-based organizations. Our team’s knowledge of science and expertise in technology help Zifo better serve our customers around the globe, including 18 of the Top 20 Biopharma companies.

We look for Science – Biotechnology, Pharmaceutical Technology, Biomedical Engineering, Microbiology etc. We possess scientific and technical knowledge and bear professional and personal goals. While we have a “no doors” policy to promote free access within, we do have a tough door to walk in.We search with a two-point agenda – technical competency and cultural adaptability.

We offer a competitive compensation package including accrued vacation, medical, dental, vision, 401k with company matching, life insurance, and flexible spending accounts.

If you share these sentiments and are prepared for the atypical, then Zifo is your calling!

Zifo is an equal opportunity employer, and we value diversity at our company. We do not discriminate on the basis of race, religion, color, national origin, gender, sexual orientation, age, marital status, veteran status, or disability status.