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APR 21, 2020 10:30 AM PDT

Long HiFi Reads for High-Quality Genome Assemblies

Sponsored by: PacBio
C.E. Credits: P.A.C.E. CE Florida CE
Speaker
  • Chief Scientific Officer, Pacific Biosciences
    Biography
      Jonas Korlach was appointed Chief Scientific Officer of Pacific Biosciences in July 2012. He was previously a Scientific Fellow, supporting commercial development of the PacBio RS II system and performing research aimed at developing new applications for SMRT technologies. He co-invented the SMRT technology with Stephen Turner, Ph.D., Pacific Biosciences Founder and Chief Technology Officer, when the two were graduate students at Cornell University.

      Dr. Korlach joined Pacific Biosciences as the company's eighth employee in 2004. Previously, he was a Postdoctoral Researcher at Cornell University. Dr. Korlach is the recipient of multiple grants, an inventor on 70 issued U.S. patents and 61 international patents, and an author of over 100 scientific studies on the principles and applications of SMRT technology, including publications in Nature, Science, and PNAS. In 2013, Dr. Korlach was honored by the Obama White House as an Immigrant Innovator "Champion of Change." He received both his Ph.D. and his M.S. degrees in Biochemistry, Molecular and Cell Biology from Cornell, and received M.S. and B.A. degrees in Biological Sciences from Humboldt University in Berlin, Germany.

    Abstract

    The introduction of PacBio HiFi sequence reads, which are both long (up to 25 kb currently) and accurate (>99%) at the individual single-molecule sequence read level, has allowed for advances in de novo genome assemblies. I will briefly review the characteristics of HiFi read data obtained with the Sequel II System, followed by examples of high-quality genome assemblies for human, plant and animal genomes. I will highlight the different aspects of evaluating genome assemblies (contiguity, accuracy, completeness and allelic phasing) and illustrate their high quality by examples of resolving centromeres, telomeres, segmental duplications and other previous difficult to resolve regions. I will also present on advances with regard to reducing the DNA input requirements (down to 5 ng for some of the presented examples) to allow for the sequencing of single individuals of small organisms, and summarize the latest advances in using full-length RNA seq (Iso-Seq) for genome annotation.

    Learning Objectives:

    1. Understand the characteristics of HiFi sequence reads

    2. Understand the latest advances in de novo genome assemblies using HiFi read data for high-quality (contiguous, accurate and complete) human, plant and animal assemblies

    3. Learn about advances in reducing the DNA input requirements for sequencing single individuals of small organisms


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