Plant Pangenome Algorithms Demystified

By the end of the workshop, attendees will: 

• Understand the basic concepts behind pan-genome algorithms and data structures without needing to be an algorithms specialist. 

• Understand how three commonly used pan-genome approaches work under the hood. 

• Understand the pros and cons of different approaches and how these relate to different research questions. 

• Understand how pan-genome graphs can be used as a database of genetic variation to answer biological questions. 

• Be introduced to existing pan-genomic resources, including Metagraph and its searchable collection of pan-genome graphs. 

• Gain practical experience exploring and querying a pan-genome graph. 

• Be better equipped to frame a biological question in a way that can be addressed using pan-genomic approaches. 

The workshop is aimed at plant genomics researchers who are interested in using pan-genomes and want to develop a better understanding of the approaches, tools and resources available to them. 

 

It will be particularly relevant for: 

• Plant geneticists and genomics researchers 

• Bioinformaticians working with plant genomic data 

• Researchers considering building or using a pan-genome 

• PhD students and early-career researchers working with pan-genomic approaches 

• Researchers who want to understand the available tools and approaches before committing significant computational time and resources 

 

No specialist background in algorithm design is assumed.

1. Pangenome algorithms, explained simply 
An accessible introduction to algorithms and data structures in the context of pan-genomics, followed by a breakdown of three commonly used approaches and how they work under the hood. 

2. Choosing the right approach 
Looking at the pros and cons of each approach and why there isn't one solution that is best for every research question. 

3. From algorithms to biological questions 
Exploring the question that should come first: What are you actually trying to find out? Looking at how different biological questions, including variant and trait discovery, can influence the approach you take. 

4. Exploring Metagraph 
An introduction to Metagraph, its online server and its collection of searchable pan-genome graphs. 

5. Practical example 
A hands-on example led by you and Sam, giving participants the opportunity to explore a pan-genome graph and see how it can be queried to answer biological questions. 

6. Bringing it together 
Recap of the key concepts, resources and considerations attendees can take away and apply to their own research.