APGAP is a Google Cloud-based application designed to centralize and optimize actionable use of pathogen genomic data for public health across Arizona.

Leveraging the Seqera platform, APGAP enables efficient, secure, and collaborative bioinformatics workflows for analysis and surveillance. The platform empowers rapid, high-quality data analysis and management for the Arizona public health genomics community, including state and local health departments, universities, and external laboratory partners.

Data standardization and submission

  • Centralized intake and quality assurance for pathogen sequence data from all contributing Arizona labs.
  • Uniform metadata requirements and quality metrics ensure reliable dataset production.
  • Integrated support for uploading sequences to national repositories (e.g., NCBI) for broader data sharing and research integration.
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Data processing and analysis

  • Nextflow is an open-source tool available for running bioinformatics workflows.
  • Seqera centralizes, streamlines, and automates Nextflow pipeline management.
  • Seqera provides customizable interactive analysis environments: launch Jupyter Notebook, RStudio, VS Code, and Xpra sessions for exploratory analysis.
  • Seqera’s Wave tool enables customization and provisioning of containers. 
  • MultiQC enables summaries and visualization of run stats across analyses.
  • Seqera provides an AI chat agent to help users explore, build, and debug analysis pipelines, accelerating onboarding and troubleshooting for bioinformatics teams.
  • Superset is available for creating visualizations, reports, and dashboards.

Collaboration and accessibility

  • Provides collaborative workspaces for multi-institution genomics research projects.
  • Enables code and pipeline sharing among users via Seqera and a dedicated GitHub org.
  • Accessible via both command line (CLI) and web browser interfaces.
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Security and access control

  • Strong governance framework for managing user permissions and data sharing agreements between all participating organizations.
  • Permission-based access and role-specific data security measures.

Reproducibility and provenance

  • Provenance of all data, pipelines, tools, and compute environments is tracked, promoting reproducibility and auditability.
  • Promotes sustainability and adaptability for future public health needs.
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Get in touch

Send us a message for questions, support, or to get access to the platform as a new user.

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