Bioinformatics Software Engineer

The Opportunity

The Software Engineering team at the Chan Zuckerberg Biohub SF works at the intersection of engineering and cutting-edge scientific research. We work on a diverse range of projects, from core internal infrastructure tools, to innovative data visualization tools and novel computer vision models. We are seeking a Bioinformatics Software Engineer to lead the development of our core internal bioinformatics pipelines. This position will be responsible for designing, implementing, and maintaining these pipelines, in collaboration with the data science and genomics teams, and with a heavy emphasis on Next Generation Sequencing. This is an exciting opportunity to contribute to ambitious, world-class scientific research projects in a highly collaborative and well-funded scientific environment.

What You'll Do

• Design, develop, and test new bioinformatics pipelines and maintain existing ones
• Collaborate with key stakeholders to elucidate, understand, and document pipeline specifications and maintenance needs
• Develop tooling to automate pipelines when appropriate, emphasizing quality, reproducibility, and efficiency
• Facilitate clear and effective communication around pipeline development across genomics, software engineering, data science, and scientific computing teams
• Create and update technical documentation on pipelines, procedures, best practices, etc.

What You'll Bring

Essential –

• Bachelor’s degree in biology, computational biology, bioinformatics, engineering, computer science, information systems, or a related field from an accredited college or university
• 3+ years of relevant work experience, post-bachelor’s, in engineering-centric bioinformatics roles
• Solid understanding of genomics, genetics, and molecular biology concepts related to NGS technologies and data analysis
• Extensive hands-on experience with standard bioinformatics workflows, including demultiplexing (e.g. bcl2fastq, Sabre), read alignment (e.g. CellRanger, kallisto, HISAT2, salmon), variant calling, and annotation
• Extensive hands-on experience with pipeline development tools such as Nextflow and Snakemake
• Experience with Illumina binaries
• Proficiency in a major programming language such as Python or Java
• Experience with UNIX/Linux and high performance computing (HPC) environments
• Familiarity with professional software development best practices (testing, documentation, version control, CI/CD pipelines)
• Strong problem-solving skills and the ability to troubleshoot complex data analysis issues
• Excellent written and oral communication skills and an ability to express technical concepts in an accessible way 

Nice to have - 

• Experience with AWS
• Experience with PacBio tools and data
• Experience with single-cell sequencing and spatial transcriptomics datasets
• Track record of contributions to open-source software projects related to bioinformatics

The Chan Zuckerberg Biohub Network requires all employees, contractors, and interns, regardless of work location or type of role, to provide proof of full COVID-19 vaccination, including a booster vaccine dose, if eligible, by their start date. Those who are unable to get vaccinated or obtain a booster dose because of a disability, or who choose not to be vaccinated due to a sincerely held religious belief, practice, or observance must have an approved exception prior to their start date.

Compensation

• Software Engineer II = $100,000 - $137,500
• Senior Software Engineer = $120,000  - $165,000

New hires are typically hired into the lower portion of the range, enabling employee growth in the range over time. To determine starting pay, we consider multiple job-related factors including a candidate’s skills, education and experience, market demand, business needs, and internal parity. We may also adjust this range in the future based on market data. Your recruiter can share more about the specific pay range during the hiring process.