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Advancement: Mapping to Pangenome Graphs

Speaker Name: 
Xian Hui Chang
Speaker Title: 
PhD Student
Speaker Organization: 
Biomolecular Engineering & Bioinformatics PhD
Start Time: 
Friday, January 29, 2021 - 1:00pm
End Time: 
Friday, January 29, 2021 - 2:00pm
Location: 
Zoom - https://ucsc.zoom.us/j/93471567286?pwd=aHdUQzFrZ09mNXVQbm1EenNZaFFVZz09 - Passcode: 126859

Abstract: The human reference genome is one of the most important resources in biological research, but its utility as a reference for all people is limited due to its lack of diversity. Pangenomes are an alternative representation of genomes that incorporate genetic variations from a population of individuals. Using a pangenome as a reference can mitigate the bias incurred by using the current standard reference genome, but because of the increased size and complexity of pangenomes, tools that use them tend to be slower and less reliable than tools that use standard references. I will develop several computational tools for working with pangenomes. First, I will present an index structure and algorithms for calculating distance between loci in a pangenome, which I use in a tool for mapping sequencing reads to a pangenome. Finally, I will present an algorithm for comparing two pangenomes by mapping them to each other.

Event Type: 
Adancement/Defense
Advisor: 
Benedict Paten
Graduate Program: 
Biomolecular Engineering & Bioinformatics PhD