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Nextflow Bioinformatics Jobs in California (NOW HIRING)

Tempus

Bioinformatics Scientist

Redwood City, CA · On-site

We are seeking a highly motivated and capable Bioinformatics Scientist to join our Liquid Biopsy ... tools (Nextflow, Snakemake) * Proven scientific reputation as demonstrated by scientific ...

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)

Tempus

Bioinformatics Scientist

Redwood City, CA · On-site +1

We are seeking a highly motivated and capable Bioinformatics Scientist to join our Liquid Biopsy ... tools (Nextflow, Snakemake) * Proven scientific reputation as demonstrated by scientific ...

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 ...

Transcripta Bio

Computational Biologist

Palo Alto, CA · On-site

Develop, maintain, and optimize reproducible bioinformatics pipelines for processing, QC, and ... Experience building and running reproducible workflows using tools such as Snakemake, Nextflow, or ...

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Nextflow Bioinformatics information

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 skills and qualifications are needed to thrive as a Nextflow bioinformatics specialist?

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 common challenges 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 are popular job titles related to Nextflow Bioinformatics jobs in California? For Nextflow Bioinformatics jobs in California, the most frequently searched job titles are:
What job categories do people searching Nextflow Bioinformatics jobs in California look for? The top searched job categories for Nextflow Bioinformatics jobs in California are:
What cities in California are hiring for Nextflow Bioinformatics jobs? Cities in California with the most Nextflow Bioinformatics job openings:
Nextflow Bioinformatics jobs near you
Infographic showing various Nextflow Bioinformatics job openings in California as of August 2026, with employment types broken down into 63% Full Time, 33% Part Time, 2% Temporary, and 2% Contract. Highlights an 54% Physical, 3% Hybrid, and 43% Remote job distribution.

Senior Bioinformaticist - Information Services (Hybrid Role)

Rady Children's Hospital-San Diego

San Diego, CA • On-site

$52.95 - $72.81/hr

Full-time

Posted 24 days ago

Rady Children's Hospital rating

8.2

Company rating: 8.2 out of 10

Based on 46 frontline employees who took The Breakroom Quiz

97th of 1,055 rated hospitals

Job description

HYBRID ROLE. Will need to be on campus half the time.
JOB SUMMARY:
The Senior Bioinformaticist is a senior-level individual contributor responsible for helping deploy, maintain, and evolve the bioinformatics framework supporting a high-throughput, ultra-rapid turnaround whole genome sequencing clinical environment. This role focuses primarily on germline genomics pipelines, population genomics analysis, and the continuous improvement of productiongrade bioinformatics workflows.
This position will work as part of a team to build and maintain scalable bioinformatics infrastructure using modern technologies in compute infrastructure, data storage, and genomic analytics, with a strong emphasis on automation, reproducibility, and integration across systems.
In addition to maintaining clinical pipelines, this role will contribute to research and innovation initiatives, exploring new computational approaches, emerging genomic technologies, and AI/ML methods applied to genomic data.
The environment is highly cross-functional, with strong collaboration across clinicians, bioinformaticians, software engineers, and researchers, as well as partnerships with biotechnology companies, academic institutions, and national or international research programs.
MINMUM QUALIFICATIONS:
Master's Degree
Experience analyzing next-gen sequencing data from raw sequencing output (BCL/FASTQ) through alignment, variant calling, annotation, and prioritization for whole genome or exome sequencing data.
Experience developing, maintaining, and troubleshooting automated bioinformatics pipelines supporting high-throughput genomic analysis in production or research environments.
Experience working with and understanding of NGS analysis tools like Dragen, BWA,, GATK,DeepVariant, Samtools, bcftools, Picard, Annovar, VEP, or similar tools
Experience with Unix/Linux operating system and software development using any of Ruby, Python,Perl, Bash
Experience working with large-scale computational environments, including HPC or distributedcompute systems, and workflow orchestration tools (e.g., Nextflow, Snakemake, WDL, Cromwell, orsimilar frameworks)
PREFERRED QUALIFICATIONS:
Ph.D
Experience in CNV and SV detection tools and interpretation of complex genomic variation.
Previous experience working in a CAP/CLIA environment
Previous experience with cloud-based development or analysis and performing benchmarking of bioinformatics tools
Experience applying machine learning or AI approaches to genomics, phenomics, or biomedical datasets.
Experience analyzing multi-omics datasets, including RNA-seq, long-read sequencing, transcriptomics, proteomics, or related genomic technologies
The current salary range for this position is $52.95 to $72.81
Rady Children's Hospital is committed to compensation that is externally competitive and internally equitable. We demonstrate this commitment by conducting regular market reviews to remain competitive with organizations of similar size in the nonprofit, healthcare sector. The range listed above does not represent the full salary range for the position but is the expected hiring range for qualified candidates. Compensation decisions consider a variety of factors including experience, education, licensure, unique skillsets, organizational need, and internal equity. This posting will remain open from the "date posted" until the hiring manager has determined there is a sufficient applicant pool or until the position is filled.

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