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Nextflow Bioinformatics Jobs in San Rafael, CA (NOW HIRING)

Mithrl

Bioinformatics Engineer, Pipelines

San Francisco, CA · On-site

$150K - $200K/yr

You will architect Nextflow and nf-core style pipelines, implement modality-specific validation and ... Design and maintain production grade bioinformatics pipelines for a wide range of data modalities ...

Mithrl

Bioinformatics Engineer, Pipelines

San Francisco, CA · On-site

$150K - $200K/yr

You will architect Nextflow and nf-core style pipelines, implement modality-specific validation and ... Design and maintain production grade bioinformatics pipelines for a wide range of data modalities ...

MyOme

Bioinformatics Software Engineer

San Francisco, CA

$130K - $160K/yr

... Nextflow, Snakemake, WDL, CWL). * Proven experience optimizing and scaling bioinformatics pipelines for performance and reliability. * Proficient in Python, with bonus points for experience in other ...

Profluent

Lead Bioinformatics Scientist, NGS

Emeryville, CA · On-site +1

$160K - $230K/yr

In this role, you'll architect core bioinformatics infrastructure, define analytical strategy, and ... Expertise with workflow orchestration tools (Nextflow, Snakemake) and cloud environments (GCP, AWS)

Vivodyne

Senior Bioinformatician

San Francisco, CA · On-site

... workflow orchestration (Nextflow, Snakemake, or equivalent) that are reproducible, version ... Ph.D. in Computational Biology, Bioinformatics, Genomics, Systems Biology, Biostatistics, or a ...

Vivodyne

Senior Bioinformatician

San Francisco, CA · On-site

... workflow orchestration (Nextflow, Snakemake, or equivalent) that are reproducible, version ... Ph.D. in Computational Biology, Bioinformatics, Genomics, Systems Biology, Biostatistics, or a ...

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All JobsNextflow Bioinformatics JobsNextflow Bioinformatics Jobs in San Rafael, CA

Nextflow Bioinformatics information

See San Rafael, CA salary details

$66.3K

$105.3K

$166.6K

How much do nextflow bioinformatics jobs pay per year?

As of Aug 3, 2026, the average yearly pay for nextflow bioinformatics in San Rafael, CA is $105,311.00, according to ZipRecruiter salary data. Most workers in this role earn between $75,200.00 and $144,400.00 per year, depending on experience, location, and employer.

What is the difference between Nextflow Bioinformatics vs Bioinformatics Analyst?

AspectNextflow BioinformaticsBioinformatics Analyst
CredentialsTypically requires a degree in bioinformatics, computer science, or related fields; familiarity with scripting and workflow management toolsUsually holds a degree in bioinformatics, biology, or related disciplines; strong analytical and programming skills
Work EnvironmentResearch labs, biotech companies, or academic institutions; focuses on developing and executing computational workflowsData analysis in research or clinical settings; interprets biological data and reports findings
Industry UsageUsed in genomics, transcriptomics, and large-scale data processing projectsApplied in research, healthcare, and diagnostics to analyze biological datasets

While both roles require bioinformatics knowledge, Nextflow Bioinformatics specializes in managing and automating computational workflows using tools like Nextflow, whereas Bioinformatics Analysts focus on analyzing biological data and interpreting results. The roles often overlap but differ in technical focus and responsibilities.

What are the key skills and qualifications needed to thrive as a Nextflow Bioinformatics specialist, and why are they important?

To thrive as a Nextflow Bioinformatics specialist, you need a strong background in bioinformatics, scripting languages (such as Python or Bash), and experience with workflow management systems, often supported by a relevant degree in bioinformatics, biology, or computer science. Proficiency with Nextflow, containerization platforms (like Docker or Singularity), and high-performance computing environments is typically required. Problem-solving ability, strong attention to detail, and effective collaboration are critical soft skills in this role. These competencies are essential for developing reproducible, scalable analysis pipelines that drive accurate biological insights in research or clinical settings.

What are some common challenges faced when developing and maintaining Nextflow pipelines in a bioinformatics team?

One common challenge in developing and maintaining Nextflow pipelines is ensuring reproducibility and compatibility across different computing environments, such as local clusters and cloud platforms. Collaborating with team members often involves integrating diverse tools and datasets, which can introduce version conflicts or software dependency issues. Additionally, keeping pipelines up-to-date with rapidly evolving bioinformatics methods requires strong communication and regular code reviews within the team. Effective documentation and modular pipeline design can help address these challenges and streamline collaborative workflows.

What is a Nextflow Bioinformatician?

A Nextflow Bioinformatician is a specialist who uses the Nextflow workflow management system to design, implement, and maintain computational pipelines for analyzing biological data. They typically work with large-scale sequencing datasets, automating processes such as data preprocessing, alignment, variant calling, and more. Their expertise lies in combining programming skills with bioinformatics knowledge to streamline and reproduce complex analyses, often in high-performance or cloud computing environments. This role is critical for ensuring reliable, scalable, and reproducible results in genomics and other life science research.
What cities near San Rafael, CA are hiring for Nextflow Bioinformatics jobs? Cities near San Rafael, CA with the most Nextflow Bioinformatics job openings:
Nextflow Bioinformatics jobs near you

Senior Bioinformatics Scientist

CEDENT

South San Francisco, CA

Full-time

Re-posted 11 days ago

Job description

We are seeking a highly motivated and innovative Senior/Staff Bioinformatics Scientist to join our R&D team focused on synthetic biology product development. In this role, you will work at the intersection of computational and molecular biology, developing advanced DNA sequence analysis pipelines, gene design algorithms, and predictive models to optimize DNA synthesis and assembly.
You will collaborate with molecular biologists, product teams, and manufacturing engineers to refine client’s core synthetic biology platform, troubleshoot assembly challenges, and improve DNA synthesis efficiency. This position emphasizes predictive modeling, algorithm development, and data-driven approaches to enhance synthetic biology workflows.
Key Responsibilities
Synthetic Biology & DNA Assembly
  • Develop bioinformatics methods supporting DNA assembly strategies and synthetic biology workflows.
  • Apply machine learning and predictive modeling to improve DNA assembly success rates and optimize synthesis parameters.
  • Collaborate with wet-lab scientists to analyze and troubleshoot molecular biology processes.
  • Develop bioinformatics approaches for diagnosing and resolving complex DNA synthesis and assembly issues.
NGS Pipeline Development & Data Science
  • Build and maintain NGS analysis pipelines (e.g., Nextflow) to support quality control and performance tracking of synthetic biology products.
  • Leverage Oxford Nanopore Technologies (ONT), Illumina, or PacBio sequencing to analyze and optimize synthesis workflows.
  • Develop predictive models to identify challenging sequences and recommend optimizations to improve synthesis efficiency.
  • Ensure pipeline accuracy, reproducibility, and scalability in research environments.
Data Analysis & Insights
  • Apply advanced statistical and machine learning methods to evaluate improvements in synthetic biology product iterations.
  • Use Python, R, and visualization tools to generate actionable insights and present findings to stakeholders.
  • Design and implement novel bioinformatics algorithms for sequence analysis and synthetic biology applications.
Cross-Functional Collaboration
  • Partner with R&D, manufacturing, and product development teams to troubleshoot assay issues and implement data-driven solutions.
  • Support the broader Bioinformatics team by integrating synthetic biology workflows with existing genomic data processing pipelines.
  • Assist with customer-facing analyses related to synthetic biology assay performance.
Required Qualifications
  • Educational Background & Experience:
  • Bachelor’s/Master’s degree with 6–8 years of industry experience, or a Ph.D. with 3+ years of industry experience in Bioinformatics, Molecular Biology, Biochemistry, Genetics, Genomics, Computational Biology, or a related field.
  • Bioinformatics & NGS Expertise:
  • Experience with ONT, Illumina, or PacBio sequencing technologies.
  • Proficiency in workflow management tools (Nextflow, Snakemake).
  • Hands-on experience designing predictive models for sequence design & synthetic biology applications.
  • Technical Skills:
  • Expertise in Python (Pandas, NumPy, SciPy) and visualization libraries (Matplotlib, Seaborn, Plotly).
  • Experience with machine learning frameworks (scikit-learn, TensorFlow, PyTorch) applied to biological sequence data.
  • Familiarity with R, SQL, or other statistical tools.
  • Molecular Biology & Synthetic Biology Knowledge:
  • Understanding of DNA assembly, cloning techniques, and molecular biology workflows.
  • Ability to interpret experimental data and provide feedback on laboratory procedures.
Preferred Qualifications
  • Experience developing design algorithms for synthetic biology applications.
  • Familiarity with deep learning approaches for biological sequence analysis.
  • Exposure to high-throughput experimental design and laboratory automation.
  • Hands-on experience with gene synthesis and synthetic biology assay development.
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About Cedent

Sourced by ZipRecruiter

CEDENT strives to attract and retain the best people and provide an environment where they can all develop professionally and build a rewarding career. As a result, we create an inclusive environment that is rich in diversity, acknowledges each individual's uniqueness and promotes respect, personal achievement and stewardship. Our clients are global and so is CEDENT. We build and maintain a global workforce that includes people from different backgrounds, with a vast range of skills and experience all united by a common culture and commitment to help our clients achieve high performance. Cultivating a diverse workforce and inclusive work environment makes business sense. Our peoples varied skills are the talent engine that powers CEDENT, enabling it in turn to deliver the innovative solutions that help our clients outperform competitors.

Industry

It services

Company size

11 - 50 Employees

Headquarters location

Plano, TX, US

Year founded

2008

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