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Senior Software Engineer - Bioinformatics



Software Engineering
San Carlos, CA, USA
Posted on Thursday, October 5, 2023

POSITION TITLE: Senior Software Engineer - Bioinformatics (Pipelines)

POSITION LOCATION: San Carlos, CA or Austin, TX


The Pipelines Engineering team at Natera builds and maintains analytical bioinformatics pipelines to reliably translate raw genomic data into clinically actionable insights for a global patient population. We optimize development velocity across R&D and Engineering. We deliver high quality, reliable, compliant production bioinformatics pipelines and associated infrastructure with global reach and scale. And we provide Natera diagnostic tests with the “secret sauce” needed for commercial success.

The Pipelines Engineering team seeks a software / bioinformatics engineer to develop new and refine existing bioinformatics pipelines with global impact and tremendous scale. In this role you will work as an integral part of a globally distributed development team collaborating closely with R&D to develop production algorithms from statistical models and prototypes and to create data analysis tools supporting research efforts. You will also work closely with stakeholders to define product requirements and translate requirements to corresponding software designs.


  • Implement new and enhance existing functionality in our portfolio of pipelines supporting Natera’s business
  • Lead the end to end delivery of functionality, from requirements to deployment
  • Process large numerical datasets efficiently
  • Support and extend our next generation sequencing framework
  • Troubleshoot and resolve defects, craft reliable unit tests, perform code reviews and root cause analysis
  • Continue improving processes and procedures and evangelizing best practices
  • Understand and be compliant with regulatory, security and data privacy requirements


  • BS Computer Science, Bioinformatics, Information Systems, etc. MS preferred.
  • Data Structures / Algorithms Coursework


  • Containerization: Docker (preferred), Singularity
  • Orchestration: DNAnexus (preferred), SevenBridges, Azure / AWS Batch, Cromwell, Kubernetes, Toil, miniWDL, AWS Omics (preferred)
  • Orchestration Language: WDL (preferred), CWL, YAML, Nextflow, Snakemake
  • Cloud: AWS, Azure, Google, AliBaba
  • Programming Language: Python (preferred), R, Java
  • Source control: GitLab (preferred), Bitbucket, GitHub, TFS
  • Extensive analytic troubleshooting skills
  • Excellent communication and organizational skills, especially for problem solving under pressure
  • Strong technical documentation skills
  • Eagerness to acquire new skills in genetics
  • Ability to thrive in a fast-paced environment and manage multiple tasks independently

Preferred Technologies:

  • High performance computing on a local cluster
  • Bioinformatics Tools: GATK, SAMtools, bedtools, bwa, primer3, etc.
  • Security / Privacy: HIPAA, GDPR
  • Biology: Next-generation sequencing, Sanger sequencing, MLPA, PCR, Southern Blot
  • Data science: Machine learning, deep neural networks


The pay range is listed and actual compensation packages are based on a wide array of factors unique to each candidate, including but not limited to skill set, years & depth of experience, certifications and specific office location. This may differ in other locations due to cost of labor considerations.
San Carlos, CA
$147,100$184,000 USD


Natera™ is a global leader in cell-free DNA (cfDNA) testing, dedicated to oncology, women’s health, and organ health. Our aim is to make personalized genetic testing and diagnostics part of the standard of care to protect health and enable earlier and more targeted interventions that lead to longer, healthier lives.

The Natera team consists of highly dedicated statisticians, geneticists, doctors, laboratory scientists, business professionals, software engineers and many other professionals from world-class institutions, who care deeply for our work and each other. When you join Natera, you’ll work hard and grow quickly. Working alongside the elite of the industry, you’ll be stretched and challenged, and take pride in being part of a company that is changing the landscape of genetic disease management.


Competitive Benefits - Employee benefits include comprehensive medical, dental, vision, life and disability plans for eligible employees and their dependents. Additionally, Natera employees and their immediate families receive free testing in addition to fertility care benefits. Other benefits include pregnancy and baby bonding leave, 401k benefits, commuter benefits and much more. We also offer a generous employee referral program!

For more information, visit

Natera is proud to be an Equal Opportunity Employer. We are committed to ensuring a diverse and inclusive workplace environment, and welcome people of different backgrounds, experiences, abilities and perspectives. Inclusive collaboration benefits our employees, our community and our patients, and is critical to our mission of changing the management of disease worldwide.

All qualified applicants are encouraged to apply, and will be considered without regard to race, color, religion, gender, gender identity or expression, sexual orientation, national origin, genetics, age, veteran status, disability or any other legally protected status. We also consider qualified applicants regardless of criminal histories, consistent with applicable laws.

If you are based in California, we encourage you to read this important information for California residents.


Please be advised that Natera will reach out to candidates with a email domain ONLY. Email communications from all other domain names are not from Natera or its employees and are fraudulent. Natera does not request interviews via text messages and does not ask for personal information until a candidate has engaged with the company and has spoken to a recruiter and the hiring team. Natera takes cyber crimes seriously, and will collaborate with law enforcement authorities to prosecute any related cyber crimes.

For more information:
- BBB announcement on job scams
- FBI Cyber Crime resource page