Bioinformatics Engineer Jobs
Bioinformatics Engineer jobs are open across pharma, genomics, clinical research, and tech, from entry-level to staff and principal, with specializations in genomic data pipelines, computational biology, and machine learning for life sciences. See the openings below and apply to the ones that match your experience.
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Showing 5 of 22+ Bioinformatics Engineer jobs
Sr Bioinformatics Software Engineer – Pipeline Development (Remote, US)
We are looking to hire a candidate with the mentioned skill sets and experience for one of our clients within the diagnostics and pharma services company. This is contracting and REMOTE role.
Job Summary
We are seeking an experienced Senior Bioinformatics Software Engineer to design, develop, and maintain scalable, production-grade NGS bioinformatics pipelines supporting clinical diagnostics and genomic applications.
The ideal candidate will have strong hands-on experience with Nextflow, Seqera Platform, Python, AWS, Docker, and CI/CD, along with expertise in clinical-grade NGS pipeline development and regulated software environments.
Key Responsibilities
- Design, develop, and optimize scalable NGS bioinformatics pipelines for clinical diagnostic applications.
- Build and maintain workflow orchestration using Nextflow and Seqera Platform.
- Develop production-ready bioinformatics software using advanced Python programming.
- Deploy, scale, and optimize genomic analysis pipelines on AWS and AWS HealthOmics.
- Implement containerized workflows using Docker and/or Singularity.
- Develop CI/CD pipelines, automated testing, regression testing, and controlled software releases.
- Ensure reproducibility, traceability, validation, and compliance with clinical software standards.
- Collaborate with bioinformatics scientists, R&D, DevOps, and clinical teams to transition research algorithms into production environments.
- Optimize pipeline performance, scalability, reliability, and cloud infrastructure costs.
Required Qualifications
- MS or PhD in Bioinformatics, Computer Science, Engineering, or a related field.
- 7+ years of relevant experience, including 5–8+ years in bioinformatics software engineering.
- Strong hands-on experience developing NGS analysis pipelines in production environments.
- Advanced proficiency in Python and software engineering best practices.
- Strong experience with Nextflow and Seqera Platform.
- Experience deploying and scaling bioinformatics workflows on AWS.
- Hands-on experience with Docker, Git, CI/CD, and automated testing.
- Experience developing software in regulated clinical environments (ISO 13485, IEC 62304, ISO 15189, or equivalent).
- Understanding of NGS assays, genomic data processing, and clinical diagnostics.
Preferred Qualifications
- Experience with DRAGEN, Sentieon, or similar NGS analysis tools.
- Hands-on experience with AWS HealthOmics.
- Knowledge of AWS EC2, Batch, S3, and Lambda.
- Experience with oncology genomics, liquid biopsy, or molecular diagnostics.
- Familiarity with Singularity and workflow performance optimization.
Other Job Details:
- Job Type: C2C or W2.
- Duration: 6+ months with high possibility of extension.
- Location: REMOTE.
- Interviews: Video interviews.
- Docs required: ID proof will be required.
Why Should You Apply?
Work with cutting edge NGS technologies, build scalable bioinformatics pipelines and contribute to innovative cancer diagnostics using Nextflow, Python and AWS. Chance to contribute to innovative cancer diagnostics using Nextflow, Python, and AWS.
Sr Bioinformatics Software Engineer – Pipeline Development (Remote, US)
We are looking to hire a candidate with the mentioned skill sets and experience for one of our clients within the diagnostics and pharma services company. This is contracting and REMOTE role.
Job Summary
We are seeking an experienced Senior Bioinformatics Software Engineer to design, develop, and maintain scalable, production-grade NGS bioinformatics pipelines supporting clinical diagnostics and genomic applications.
The ideal candidate will have strong hands-on experience with Nextflow, Seqera Platform, Python, AWS, Docker, and CI/CD, along with expertise in clinical-grade NGS pipeline development and regulated software environments.
Key Responsibilities
- Design, develop, and optimize scalable NGS bioinformatics pipelines for clinical diagnostic applications.
- Build and maintain workflow orchestration using Nextflow and Seqera Platform.
- Develop production-ready bioinformatics software using advanced Python programming.
- Deploy, scale, and optimize genomic analysis pipelines on AWS and AWS HealthOmics.
- Implement containerized workflows using Docker and/or Singularity.
- Develop CI/CD pipelines, automated testing, regression testing, and controlled software releases.
- Ensure reproducibility, traceability, validation, and compliance with clinical software standards.
- Collaborate with bioinformatics scientists, R&D, DevOps, and clinical teams to transition research algorithms into production environments.
- Optimize pipeline performance, scalability, reliability, and cloud infrastructure costs.
Required Qualifications
- MS or PhD in Bioinformatics, Computer Science, Engineering, or a related field.
- 7+ years of relevant experience, including 5–8+ years in bioinformatics software engineering.
- Strong hands-on experience developing NGS analysis pipelines in production environments.
- Advanced proficiency in Python and software engineering best practices.
- Strong experience with Nextflow and Seqera Platform.
- Experience deploying and scaling bioinformatics workflows on AWS.
- Hands-on experience with Docker, Git, CI/CD, and automated testing.
- Experience developing software in regulated clinical environments (ISO 13485, IEC 62304, ISO 15189, or equivalent).
- Understanding of NGS assays, genomic data processing, and clinical diagnostics.
Preferred Qualifications
- Experience with DRAGEN, Sentieon, or similar NGS analysis tools.
- Hands-on experience with AWS HealthOmics.
- Knowledge of AWS EC2, Batch, S3, and Lambda.
- Experience with oncology genomics, liquid biopsy, or molecular diagnostics.
- Familiarity with Singularity and workflow performance optimization.
Other Job Details:
- Job Type: C2C or W2.
- Duration: 6+ months with high possibility of extension.
- Location: REMOTE.
- Interviews: Video interviews.
- Docs required: ID proof will be required.
Why Should You Apply?
Work with cutting edge NGS technologies, build scalable bioinformatics pipelines and contribute to innovative cancer diagnostics using Nextflow, Python and AWS. Chance to contribute to innovative cancer diagnostics using Nextflow, Python, and AWS.
See All 22 Bioinformatics Engineer Jobs
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Find Bioinformatics Engineer JobsBioinformatics Engineer Job Market
Who's Hiring
Top Industries Hiring
- Technology & Software
- Healthcare & Medical Services
- Science & Research
- Biotechnology & Pharmaceuticals
- Consulting & Professional Services
What Employers Look For
The qualifications that appear most often in bioinformatics engineer jobs.
- Bachelor's or master's degree in bioinformatics, computational biology, or a related field
- Proficiency in Python and R for genomic data analysis and pipeline development
- Experience with workflow management tools such as Nextflow, Snakemake, or WDL
- Hands-on work with NGS data types including WGS, RNA-seq, and single-cell sequencing
- Familiarity with cloud computing platforms such as AWS, GCP, or Azure for large-scale data processing
- Knowledge of bioinformatics databases and reference resources including Ensembl, NCBI, and UCSC Genome Browser
Tips for Your Bioinformatics Engineer Job Search
Tailor your resume to pipeline work
Hiring managers for bioinformatics engineer roles scan for specific pipeline tools like Nextflow, Snakemake, or WDL. List the exact workflows you've built or maintained, not just the languages. Vague entries like 'worked with genomic data' won't clear an ATS filter.
Highlight domain-specific datasets you've used
Pharma and clinical employers care whether you've worked with TCGA, GTEx, UK Biobank, or similar large-scale genomic datasets. Naming these in your resume signals hands-on experience that a general data engineer background doesn't provide.
Apply early to roles that fit
Migrate Mate lists bioinformatics engineer openings from across the United States in one place, so you can find roles that match and apply directly to each listing.
Filter openings by compute environment
Many postings distinguish between cloud-native roles (AWS, GCP, Azure) and HPC cluster environments. Knowing which stack a team uses lets you match your cloud or SLURM experience to the right opening instead of applying broadly and missing the mark.
Prepare a take-home or coding screen early
Most bioinformatics engineer interviews include a technical screen involving a real or synthetic variant-calling, alignment, or QC task. Refresh your Python or R scripting and review common file formats like VCF, BAM, and FASTQ before your first phone call.
Negotiate around compute access, not just salary
When evaluating an offer, ask about cloud compute budgets, access to proprietary datasets, and whether the team uses version-controlled pipeline repositories. These factors directly affect your day-to-day productivity and your ability to build a strong portfolio.
Bioinformatics Engineer Jobs: Frequently Asked Questions
Which companies are hiring the most bioinformatics engineers?
The companies hiring the most bioinformatics engineers right now include Quest Diagnostics, QIAGEN, and Freenome, with the largest share of openings in California, Massachusetts, and Maryland, based on current listings on Migrate Mate as of November 2026. Pharma, genomics, and clinical diagnostics companies consistently account for the highest volume of active postings.
How many bioinformatics engineer jobs are remote?
About 88% of bioinformatics engineer openings are fully remote or hybrid as of November 2026, reflecting strong demand for distributed scientific teams. Pipeline engineering, software-focused bioinformatics, and cloud infrastructure roles tend to be the most remote-friendly, while positions tied to on-site sequencing instruments or wet lab collaboration are more likely to require an in-person presence.
How do you become a bioinformatics engineer?
Start with a degree in bioinformatics, computational biology, computer science, or a life science with a strong quantitative component. Build hands-on experience writing analysis pipelines in Python or R, working with NGS data formats, and deploying workflows in cloud or HPC environments. Contributing to open-source genomics tools or publishing reproducible analyses on a public code repository strengthens your profile significantly before your first role.
How do you get hired as a bioinformatics engineer with little experience?
Focus on building a portfolio of end-to-end pipeline projects using publicly available datasets from resources like TCGA or GEO. Entry-level postings at genomics startups and academic medical centers often accept candidates who can demonstrate clean, documented code over formal industry experience. A graduate research project or a contract bioinformatics gig that produced a published or preprint result carries real weight with hiring managers in this field.
What does the bioinformatics engineer interview process look like?
Most processes start with a recruiter screen, followed by a technical phone call covering your pipeline experience and coding fundamentals. A take-home assessment is common and usually involves processing a small genomic dataset, writing a variant-calling or QC script, or reviewing someone else's Nextflow workflow. Final rounds typically include a live coding exercise and a panel interview with scientists or engineers who assess both technical depth and cross-functional collaboration skills.
Where can I find and apply to bioinformatics engineer jobs?
You can find and apply to bioinformatics engineer jobs on Migrate Mate, which lists current openings from across the United States. Search for roles that match your pipeline experience, domain focus, and preferred work setting, then apply directly to each listing. New positions are added regularly, so checking back frequently gives you the best shot at catching openings as they go live.
See All 22 Bioinformatics Engineer Jobs
Find roles that match your experience and apply in just a few clicks.
Find Bioinformatics Engineer Jobs