Episode 32: Looking behind Majora's Mask and nation wide tracking of SARS-CoV-2 genomics

The microbinfie podcast explores the development of Majora, a critical database infrastructure created during the COVID-19 pandemic to support rapid SARS-CoV-2 genome sequencing across the United Kingdom.

Join Nick Loman, Sam Nicholls, and Radosław Popławski as they discuss the development of systems to support the analysis of hundreds of thousands of SARS-CoV-2 genomes during the pandemic, notably without the use of Excel.

Learn more about MAJORA, a system for continuous integration supporting decentralized sequencing for SARS-CoV-2 genomic surveillance. You can access the preprint here. For more information, visit the COG-UK Consortium website.

Here are the main points from the episode:

1. Majora Database:

   • Majora is the central database infrastructure supporting COG-UK's sequencing efforts.
   • It connects distributed sequencing hubs, integrating sequence data and sample metadata for analysis and public database uploads.

2. Motivation for Majora:

   • The need for an agile and flexible software solution arose from the sudden demand for rapid genome sequencing during the COVID-19 outbreak.
   • Existing systems were inadequate for the distributed nature and varied sequencing protocols of COG-UK.

3. Development Timeline:

   • The work on Majora began in March 2020, with a quick response to the urgent need for a user management system.
   • Initial prototypes were developed in a matter of days, showcasing the team's rapid adaptability.

4. Technical Aspects:

   • Majora is built on Django (Python framework) and employs Nextflow for pipeline management.
   • The design prioritizes flexibility and usability, accommodating a range of sequencing techniques and protocols.

5. Integration and Testing:

   • Majora's development involved collaboration with various stakeholders and was not built in isolation.
   • Testing was primarily integration-focused, with a separate test instance called "magenta" for deployment.

6. API and Documentation:

   • The API is a central component of Majora, with initial documentation created in Markdown.
   • Transitioned to a more structured documentation using OpenAPI specifications for better maintenance and usability.
   • A web interface developed by Anthony Underwood and his team enhances user interaction, allowing users to upload metadata efficiently.

7. Community Contribution:

   • The success of Majora relies on contributions from a large consortium of approximately 400-500 individuals across various institutions.
   • Collaboration and shared expertise were vital to the rapid establishment of the system.

8. Cultural References:

   • The name "Majora" is inspired by the video game "Legend of Zelda: Majora's Mask," symbolizing its role in addressing the urgent global crisis.

Key Points

1. Majora's Origin and Purpose

• Developed rapidly in March 2020 to support COG-UK's distributed sequencing efforts
• Designed to integrate sequence data and sample metadata from multiple sequencing hubs
• Enabled flexible, agile response to the urgent need for coronavirus genomic tracking

2. Technical Development

• Built on Django with Nextflow for pipeline management
• Initially started as a user management system within days of project initiation
• Leveraged existing infrastructure like the CLIMB cloud platform

3. Collaborative Ecosystem

• Involved approximately 400-500 individuals across various institutions
• Developed through close collaboration and rapid prototyping
• Named after the video game "Legend of Zelda: Majora's Mask" symbolizing crisis response

Take-Home Messages

• Rapid bioinformatics solutions can emerge from collaborative, adaptable approaches
• Existing technological foundations are crucial for emergency response systems
• Distributed genomic surveillance requires flexible, scalable infrastructure