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Advancement: Exploring the utility of long reads in genome assembly, diplotyping, and comparative genomics

Speaker Name: 
Marina Haukness
Speaker Title: 
PhD Student
Speaker Organization: 
Biomolecular Engineering & Bioinformatics PhD
Start Time: 
Wednesday, June 3, 2020 - 10:00am
End Time: 
Wednesday, June 3, 2020 - 11:00am
Location: 
Zoom - https://ucsc.zoom.us/j/93883187262?pwd=UW42YVY5SEZROWJnTmMydjAydVZSdz09

Abstract: Despite their accuracy, next-generation DNA sequencing technologies have limited utility in analyzing ambiguous and repetitive parts of the genome due to the short length of reads. Third-generation long read DNA sequencing technologies, such as those from Oxford Nanopore Technologies (ONT) and Pacific Biosciences (PacBio), allow us to explore much more of the genome. However, new software must be developed for these analyses in order to take advantage of the increased read lengths, while mitigating errors from base-level inaccuracies. In my thesis, I propose to first explore the advantages of long reads in three areas: genotyping, haplotype phasing, and genome assembly. I will then use high-quality genomes created from long reads to perform comparative genomics analyses, focusing on identifying patterns of gene gain and loss events in primate evolution.

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