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Bioinformatics Engineering Jobs (NOW HIRING)

MyOme

Bioinformatics Software Engineer

San Francisco, CA

$130K - $160K/yr

You will combine strong engineering practices with bioinformatics expertise to develop reliable, production-grade systems that support clinical decision-making and advance precision medicine. What ...

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How much do bioinformatics engineering jobs pay per year?

As of Jun 7, 2026, the average yearly pay for bioinformatics engineering in the United States is $131,053.00, according to ZipRecruiter salary data. Most workers in this role earn between $96,000.00 and $157,000.00 per year, depending on experience, location, and employer.

What is the difference between Bioinformatics Engineering vs Bioinformatics Analyst?

AspectBioinformatics EngineeringBioinformatics Analyst
Required CredentialsBachelor's or Master's in Bioinformatics, Computer Science, or related fields; programming skillsBachelor's or Master's in Bioinformatics, Biology, or related fields; data analysis skills
Work EnvironmentResearch labs, biotech companies, healthcare institutionsResearch institutions, healthcare, pharmaceutical companies
Employer & Industry UsageDevelops tools, pipelines, and software for data analysisInterprets data, generates reports, supports research projects

Bioinformatics Engineering focuses on developing software and pipelines for data processing, requiring programming expertise. In contrast, Bioinformatics Analysts primarily interpret data and generate insights, often with a stronger emphasis on biological knowledge. Both roles are vital in biotech and healthcare industries, but they differ in technical scope and daily tasks.

What is a bioinformatics engineer?

A bioinformatics engineer is a professional who develops and applies computational tools and techniques to analyze and interpret biological data, such as DNA sequences or protein structures. They combine expertise in computer science, biology, and mathematics to create software, manage databases, and solve complex biological problems. Bioinformatics engineers often work in research, pharmaceuticals, healthcare, and biotechnology industries to help advance scientific discoveries and medical innovations.

How do bioinformatics engineers typically collaborate with biologists and data scientists in a research setting?

Bioinformatics engineers frequently work in cross-disciplinary teams, partnering closely with biologists to understand experimental goals and with data scientists to analyze complex datasets. Effective communication is key, as engineers must translate biological questions into computational workflows and interpret results in a way that is meaningful to non-technical team members. This collaborative approach not only accelerates research but also helps engineers gain a deeper understanding of biological processes, which can lead to more innovative solutions and professional growth.

What is the salary of a bioinformatics engineer?

The average salary of a bioinformatics engineer typically ranges from $70,000 to $120,000 per year, depending on experience, education, and location. Professionals with advanced skills in programming, data analysis, and familiarity with tools like Python, R, and Linux tend to earn higher salaries.

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

To thrive as a Bioinformatics Engineer, you need a solid background in biology, computer science, and statistics, often supported by a degree in bioinformatics or a related field. Familiarity with programming languages like Python or R, experience with bioinformatics tools (e.g., BLAST, GATK), and proficiency with databases and cloud computing platforms are typically required. Strong problem-solving, analytical thinking, and collaboration skills set standout professionals apart in this interdisciplinary field. These competencies are crucial for effectively analyzing complex biological data and driving innovation in life sciences research.
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Bioinformatics Engineering jobs near you
Infographic showing various Bioinformatics Engineering job openings in the United States as of May 2026, with employment types broken down into 87% Full Time, and 13% Part Time. Highlights an 69% In-person, 6% Hybrid, and 25% Remote job distribution, with an average salary of $131,053 per year, or $63 per hour.
Bioinformatics Scientist

Bioinformatics Scientist

Cube Hub, Inc.

Foster City, CA

Other

Posted 4 days ago

Job description

Job description:

Bioinformatics Engineer T2T Genome Assembly (Non-Model Organisms)

Location: Foster City CA/Hybrid (as applicable)
Duration: 12-Month Contract

We are seeking a highly skilled Bioinformatics Engineer to support the development of Telomere-to-Telomere (T2T) reference genomes for non-model organisms. This role will focus on building, optimizing, and operating long-read genome assembly and curation pipelines using PacBio HiFi and/or Oxford Nanopore sequencing data, while collaborating closely with wet-lab and computational biology teams.

Key Responsibilities

  • Design and execute genome assembly strategies for non-model organisms, including data quality assessment, genome profiling, contamination screening, and sequencing recommendations.
  • Perform long-read genome assemblies using tools such as Hifiasm, Verkko, Flye, and Canu, driving assemblies toward chromosome-scale and T2T-quality results.
  • Resolve haplotypes and complex genome structures, including highly heterozygous and polyploid genomes, utilizing approaches such as trio binning and Hi-C/Strand-seq-assisted phasing.
  • Scaffold and curate assemblies using long-range genomic data, including Hi-C, Omni-C, Strand-seq, and optical maps.
  • Identify and correct assembly errors, close gaps where feasible, and document curation decisions.
  • Evaluate assembly quality using tools such as Merqury, BUSCO, QUAST, k-mer analyses, and read-mapping approaches.
  • Develop and maintain scalable bioinformatics workflows using Nextflow, Snakemake, or WDL.
  • Deploy and manage workflows across on-premises HPC environments and AWS cloud infrastructure.
  • Generate technical reports, release documentation, and data packages for internal and external stakeholders.

Required Qualifications

  • PhD in Bioinformatics, Computational Biology, Computer Science, Genomics, or a related field.
  • Hands-on experience with de novo genome assembly using long-read sequencing technologies (PacBio HiFi and/or Oxford Nanopore).
  • Strong expertise with assembly tools such as Hifiasm, Verkko, Flye, Canu, or similar platforms.
  • Experience assessing assembly quality, troubleshooting assembly issues, and improving genome completeness.
  • Strong programming skills in Python and/or Bash within Linux environments.
  • Experience with workflow development using Nextflow, Snakemake, or WDL.
  • Experience running large-scale genomics workloads on HPC environments (Slurm, LSF, or similar).
  • Familiarity with AWS cloud services and scalable genomics computing environments.
  • Strong software engineering practices, including Git version control, testing, and documentation.

Preferred Qualifications

  • Experience working with non-model organisms and complex genomes.
  • Demonstrated success delivering chromosome-scale or T2T genome assemblies.
  • Knowledge of repeat annotation, genome annotation, and evidence-driven gene annotation workflows.
  • Experience with haplotype-resolved assemblies and advanced genome curation.
  • Publications, preprints, reference genome releases, or contributions to community genomic resources.

Nice to Have

  • RNA-Seq integration and genome annotation experience.
  • Genome browser track generation and visualization experience.
  • AWS Batch, HealthOmics, and S3 data management expertise.
  • Excellent communication skills and ability to collaborate across multidisciplinary teams.

This is an exciting opportunity to contribute to cutting-edge genomics research and help deliver high-quality reference genomes that support scientific discovery and innovation.

Apply