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Nextflow Bioinformatics Jobs (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 ...

RXinsider LTD.

$146 - $234/hr

NextFlow, Luigi, Snakemake, NextFlow preferred), version control systems (Git preferred), Cloud ... Experience with bioinformatics software and an understanding of neoantigen therapies * Proven ...

Vivo HealthStaff

Bioinformatics Scientist

Ann Arbor, MI · On-site

$170K - $190K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required. * Sequencing Data:

Vivo HealthStaff

Bioinformatics Scientist

Boston, MA · On-site

$170K - $190K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required. * Sequencing Data:

Vivo HealthStaff

Bioinformatics Scientist

Winter Park, FL · On-site

$150K - $180K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required.Sequencing Data:

Vivo HealthStaff

Bioinformatics Scientist

Winter Park, FL · On-site

$170K - $190K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required. * Sequencing Data:

Vivo HealthStaff

Bioinformatics Scientist

Boston, MA · On-site

$170K - $190K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required. * Sequencing Data:

Vivo HealthStaff

Bioinformatics Scientist

Boston, MA · On-site

$170K - $190K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required.Sequencing Data:

Vivo HealthStaff

Bioinformatics Scientist

Ann Arbor, MI

$170K - $190K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required. * Sequencing Data:

Vivo HealthStaff

Bioinformatics Scientist

Boston, MA

$170K - $190K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required. * Sequencing Data:

Vivo HealthStaff

Bioinformatics Scientist

Boston, MA · On-site

$170K - $190K/yr

Significant, hands-on experience with Nextflow and Docker is critical for pipeline development. Proficiency with standard bioinformatics tooling (Python, Linux, Git) is required.Sequencing Data:

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Nextflow Bioinformatics information

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$59.5K

$94.5K

$149.5K

How much do nextflow bioinformatics jobs pay per year?

As of Aug 27, 2026, the average yearly pay for nextflow bioinformatics 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 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 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 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.

More about Nextflow Bioinformatics jobs

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Cities with the most Nextflow Bioinformatics job openings:

What states have the most Nextflow Bioinformatics jobs?

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What job categories do people searching Nextflow Bioinformatics jobs look for?

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Nextflow Bioinformatics jobs near you
Infographic showing various Nextflow Bioinformatics job openings in the United States as of August 2026, with employment types broken down into 46% Full Time, 53% Part Time, and 1% Contract. Highlights an 41% Physical, 2% Hybrid, and 57% Remote job distribution, with an average salary of $94,474 per year, or $45.4 per hour.

Bioinformatics Engineer, Pipelines

Mithrl

San Francisco, CA • On-site

$150K - $200K/yr

Full-time

Medical, Dental, Vision, Retirement

Re-posted 29 days ago

Job description

ABOUT MITHRL
We imagine a world where new medicines reach patients in months, not years, and where scientific breakthroughs happen at the speed of thought.
Mithrl is building the world's first commercially available AI Co-Scientist. It is a discovery engine that transforms messy biological data into real insights in minutes. Scientists ask questions in natural language, and Mithrl responds with analysis, novel targets, hypotheses, and patent-ready reports.
Our traction speaks for itself:
  • 12X year-over-year revenue growth
  • Trusted by leading biotechs and big pharma across three continents
  • Driving real breakthroughs from target discovery to patient outcomes.

ABOUT THE ROLE
We are looking for a Lead Bioinformatics Pipeline Engineer to build and scale Mithrl's multi modal scientific processing pipelines. You will own the workflows that transform raw biological data into clean, reproducible outputs that power Mithrl's AI Co-Scientist. These workflows include microarray, imaging, spatial transcriptomics, genomics, epigenomics, flow cytometry, and more.
This role sits at the center of our technical stack. You will architect Nextflow and nf-core style pipelines, implement modality-specific validation and QC layers, and collaborate with the Tabular Data Team and Knowledge Curation Team to ensure downstream data harmonization, variable ID mapping, and schema alignment. Your work ensures that scientists can ask questions and receive accurate data-backed answers instantly.
If you enjoy building robust scientific workflows and want to work on high impact problems, you will thrive here.
WHAT YOU WILL DO
  • Design and maintain production grade bioinformatics pipelines for a wide range of data modalities, including microarray, cell painting, WGS and WES, spatial transcriptomics, flow cytometry, ATAC-seq, and methyl-seq
  • Build workflows using Nextflow, nf-core modules, or similar engines with a focus on reproducibility, validation, and scalability
  • Implement quality control, validation, and provenance tracking for all supported modalities
  • Collaborate with the Tabular Data Team to ensure pipeline outputs map cleanly into Mithrl's internal schemas, including variable ID coercions, metadata normalization, and feature name harmonization
  • Work with the Knowledge Curation Team to align outputs with reference genomes, annotations, and biological ontologies
  • Produce structured output artifacts so users can download processed data and supporting metadata directly through the platform

WHAT YOU BRING
Required Qualifications
  • 6 to 8 years of experience in bioinformatics workflow engineering or computational biology
  • Strong experience with Nextflow, nf-core, WDL, CWL, Snakemake, or similar workflow systems
  • Proficiency in Python or R for data processing, QC, and pipeline logic
  • Hands-on experience building pipelines for multiple biological data types, including genomics, single cell, imaging, flow cytometry, spatial data, or epigenomics
  • Ability to design pipelines that are reproducible and containerized using Docker or Singularity
  • Strong understanding of secondary and tertiary data layers and how they integrate with downstream analysis systems
  • Experience integrating pipeline outputs with data stores, schemas, or ML-ready formats

Nice to Have
  • Experience executing pipelines in cloud environments such as AWS Batch, ECS, Tower, or Nextflow Cloud
  • Experience with imaging workflows such as CellProfiler, DeepCell, or Squidpy
  • Familiarity with genomic reference databases, annotation formats, and biological ontologies
  • Previous work in a tech bio startup, biotech R&D group, or scientific software company

WHAT YOU WILL LOVE AT MITHRL
  • You will build the core pipelines that transform raw biological data into insights used by the AI Co-Scientist
  • Team: Join a tight-knit, talent-dense team of engineers, scientists, and builders
  • Culture: We value consistency, clarity, and hard work. We solve hard problems through focused daily execution
  • Speed: We ship fast (2x/week) and improve continuously based on real user feedback
  • Location: Beautiful SF office with a high-energy, in-person culture
  • Benefits: Comprehensive PPO health coverage through Anthem (medical, dental, and vision) + 401(k) with top-tier plans

We encourage you to apply even if you do not believe you meet every single qualification. Not all strong candidates will meet every single qualification as listed. Research shows that people who identify as being from underrepresented groups are more prone to experiencing imposter syndrome and doubting the strength of their candidacy, so we urge you not to exclude yourself prematurely and to submit an application if you're interested in this work. We think AI systems like the ones we're building have enormous social and ethical implications. We think this makes representation even more important, and we strive to include a range of diverse perspectives on our team.

Apply