Bioinformatics Software Engineer
Posted on 9/18/2023
Chan Zuckerberg Biohub

51-200 employees

Locations
San Francisco, CA, USA
Experience Level
Entry
Junior
Mid
Senior
Expert
Desired Skills
AWS
Data Analysis
Data Science
Java
Linux/Unix
Python
CategoriesNew
Software Engineering
Biology & Biotech
Requirements
  • 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
  • Resources to disrupt and innovate at the frontiers of our knowledge of biology and disease
  • A collegial and collaborative environment consisting of diverse expertise
  • Existing collaborations within CZ Biohub: Technology Platforms (Bioengineering, Computational Microscopy, Data Science, Genomics & Mass Spectrometry), Infectious Disease, and Quantitative Cell Science
  • Access to collaborators, resources and facilities at our three partner universities (Stanford, UC Berkeley, and UC San Francisco) and at partner organizations in the Bay Area and beyond
  • Competitive compensation and benefits commensurate with the experience
Responsibilities
  • 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
Desired Qualifications
  • 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