Bioinformatics Analyst II

Ginkgo believes that if we are to grow a thriving, sustainable bioeconomy, we must also grow a new market in biosecurity. Our biosecurity and public health initiative, Concentric by Ginkgo, launched a nationwide emergency response to the COVID-19 pandemic, providing end-to-end pathogen monitoring services to schools, communities, and travelers. As we continue to scale Concentric, our work is also evolving into new and exciting directions, from global expansion to the integration of new technologies and capabilities, including our Traveler-Based Genomic Surveillance Plan with the CDC. 

Role Introduction:

We are seeking a motivated bioinformatician to join our growing Biosecurity Team and be a part of implementing innovative biosecurity solutions. Specifically, you bring subject matter expertise in high-throughput sequencing data, bioinformatics, pipeline development, and high performance computing to help the Biosecurity Division’s grow biomonitoring programs. Your responsibilities will include engineering pipelines, analyzing sequencing data, and supporting the development of long-term biosecurity initiatives. In this role you will interface with key teams in the Ginkgo Bioworks Foundry and Biosecurity Divisions to ensure program success through high quality deliverables and appropriately resourced activities. You are a cross-functional team player, bringing diverse perspectives to our interdisciplinary team, and poised to develop the future of biosecurity.

Responsibilities

• Support Ginkgo’s Biosecurity Teams with your technical expertise in bioinformatics
• Support data management across biosecurity programs 
• Support pipeline development & improvement for biosecurity, biosurveillance, and new sequence based tools
• Support retrieving, parsing, and processing structured and unstructured data
• Assist in management of data pipelines across various stages of the lifecycle from exploration to production including logging and monitoring issues & bugs
• Interface with software engineers to create and implement NGS data analysis pipelines for production use
• Analyze & benchmark sequencing data from multiple NGS technologies 

Minimum Requirements

• BS + minimum 2 years relevant experience, OR Master’s degree in related discipline 
• Proficient in at least one software programming language (Python)
• Proficient in workflow management software (Nextflow, Docker)
• Proficient in distributed computing (AWS/Google Cloud) 
• Proficient in collaborative software development (version control systems, test-driven development, and good documentation habits)
• First-hand technical experience in at least two of the following disciplines:  bioinformatics, sequence analysis, comparative genomics, genome assembly & annotation, statistics, probabilistic modeling, machine learning, or quantitative modeling of biological systems
• Demonstrated ability to meet the demands of multiple concurrent projects, and work efficiently in a fast-paced, high-growth environment
• Ability to adapt to changing priorities and pivot as needed in a fast-paced environment
• Strong communication skills, with the ability to effectively convey project plans and complex technical details to a wide range of internal teams, executive leadership, and external customers
• Strong curiosity for, and comfort working in, areas of biology & biosecurity previously unknown to you (and, at times, unknown to your peers)

Preferred Capabilities and Experience

• At least one year of industrial experience in computational biology/bioinformatics role
• Experience analyzing and benchmarking outputs from multiple sequencing technologies: Illumina, Oxford Nanopore, PacBio
• Experience with NGS QA/QC and tracking associated metrics
• Direct sequencing and bioinformatics experience with varied pathogen types (e.g. viral, bacterial, fungal)
• Extensive experience with many or all of the following:  Python, bash/unix scripting, Snakemake, Nextflow, airflow, CWL, relational databases (SQL), distributed computing (AWS/Google Cloud), Docker, software version control (git)
• Experience with data visualization and dashboarding (e.g., Tableau, Evidence, D3, or other)
• Experience working with JIRA, SCRUM, and agile methodologies

Total compensation for this role is market driven, with a starting salary of $67k+, as well as company stock awards.  Base pay is ultimately determined based on a candidate's skills, expertise, and experience.  We also offer a comprehensive benefits package including medical, dental & vision coverage, health spending accounts, voluntary benefits, leave of absence policies, Employee Assistance Program, 401(k) program with employer contribution, 8 paid holidays in addition to a full-week winter shutdown and unlimited Paid Time Off policy.