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Bacterial Genome Sequencing from Low Input DNA Using Hybrid Nanopore and Illumina Sequencing

3:30 pm - 4:30 pm, March 29, 2017

The Department of Biopharmaceutical Sciences Presents:

"Bacterial Genome Sequencing from Low Input DNA Using Hybrid Nanopore and Illumina Sequencing"

Jean-Francois Pombert, Ph.D
Assistant Professor
Department of Biology
Illinois Institute of Technology
Chicago, IL

March 29, 2017 (Wednesday)
3:30 PM – 4:30 PM

Room 134-3 COP
Room E226 ROCKFORD
833 S. Wood Street
Chicago, IL

Abstract:  The advent of high-throughput short read sequencing combined with the recent rise of long read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore have led to an explosion of bacterial genomes being released in public repositories. However, the distribution of genomes present in those repositories is skewed towards organisms that are amenable to culturing and those that cannot (or should not in the case of dangerous pathogens) be cultured are often underrepresented. Culture-free methods require sequencing technologies capable of starting from tiny amounts of input DNA. While Illumina libraries starting from 1 ng of DNA have been available for a few years, bacterial genomes sequenced with short read technologies are often incomplete when repetitive elements are present, as those elements cannot be resolved without additional information. The PacBio platform has proven to be an excellent platform to generate complete, high-quality bacterial genomes but the amounts of material required (in the 5-10 ug range) limits what can be done on this platform. One of the appeals of the latest long read technology from Oxford Nanopore is that it can starts from minute amounts of DNA. We used a hybrid illumina/nanopore approach to sequence various staphylococcal and streptococcal species from limited amounts of genomic DNA. This approach was simple enough to be performed by undergraduates with limited supervision. I will discuss the pros and cons of this approach.

Event Details

Location: College of Pharmacy
Room: 134-3/Rockford E226
Address:
833 S. Wood St.
Chicago, IL

Sponsor: Department of Biopharmaceutical Sciences

Contact Name: Celina Tejada
Contact Email: tejada@uic.edu
Contact Phone: 312-996-0888

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Date Posted: Thu, Jan 12
Date Updated: Thu, Jan 12

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