VCF Files for Population Genomics: Scaling to Millions of Samples

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VCF Files for Population Genomics: Scaling to Millions of Samples

VCF Files for Population Genomics: Scaling to Millions of Samples

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Codeathon Outcomes:

This codeathon concluded on August 4th, 2023. To see what teams accomplished, check out their GitHub repositories and/or watch the recorded final presentations.

Codeathon Description:

NCBI and NIAID co-hosted a codeathon, VCF Files for Population Genomics: Scaling to Millions of Samples, held virtually from July 31st to August 4th, 2023. VCF, or Variant Call Format Files, are a widely used file for storing information about genetic variations across multiple samples. This event aimed to bring together experts in viral evolution, molecular epidemiology, and population genomics to explore methods for computing on the scale of millions of records using VCF files as inputs, with SARS-CoV-2 VCFs serving as a case study. 

We invited both programmers and non-programming subject matter experts to apply for this event. During the week-long codeathon, teams of 5-8 people collaborated virtually to design visualizations and write software to address the following objectives: 

  • Explore the use of SARS-CoV-2 variant call format (VCF) files as input to downstream applications such as viral classification, characterization, and phylogenetic tree construction. 
  • Estimate intra-host sequence diversity and predict emerging new variants of SARS-CoV-2 using VCFs as input. 
  • Streamline processes to assess the current therapeutic and preventative options using VCFs. For example, assessing genome-scale responses to vaccines or therapeutics.  
  • Enhance and facilitate the data clustering process and modeling for predictions using VCFs. 

The codeathon was designed to be cooperative rather than competitive, and teams shared ideas and technical expertise. 

Team products are publicly available through the NCBI Codeathons GitHub Organization.

Event registration closed.
 

Date And Time

07-31-2023 @ 12:00 PM (EDT) to
08-04-2023 @ 03:00 PM (EDT)
 

Registration End Date

06-17-2023
 

Location

Online event
 

Event Types

 

Event Category

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