Highly Accurate Consensus Sequence and Genome Assembly using PacBio® RS Sequence Data

Date Thursday November 29, 2012 at 4:00 PM
Location 13-105 Center for the Health Sciences (CHS)
Speaker David Alexander, Ph.D., Senior Algorithms Engineer, Pacific Biosciences, Menlo Park, CA
Sponsoring Dept UCLA Biomathematics
Abstract Pacific Biosciences’ single molecule real-time (SMRT®) DNA sequencing platform provides extremely long read lengths and a rich profile of DNA template modifications, enabling advances in de novo genome assembly and epigenetic studies. In this talk I will discuss some of the basic mathematical models behind genome assembly, and then give an overview of our hierarchical genome assembly procedure (HGAP). After a brief overview of the properties of PacBio sequence data, I will describe our algorithm, Quiver, for highly accurate consensus sequence determination, which can generate finished assemblies with accuracies exceeding 99.999%.
Flyer david_alexander_20121129.pdf