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    Comparison of long read sequencing technologies in interrogating bacteria and fly genomes

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    Author
    Tvedte, Eric S
    Gasser, Mark
    Sparklin, Benjamin C
    Michalski, Jane
    Hjelmen, Carl E
    Johnston, J Spencer
    Zhao, Xuechu
    Bromley, Robin
    Tallon, Luke J
    Sadzewicz, Lisa
    Rasko, David A
    Dunning Hotopp, Julie C
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    Date
    2021-04-19
    Journal
    G3: Genes, Genomes, Genetics
    Publisher
    Oxford University Press
    Type
    Article
    
    Metadata
    Show full item record
    See at
    https://doi.org/10.1093/g3journal/jkab083
    Abstract
    The newest generation of DNA sequencing technology is highlighted by the ability to generate sequence reads hundreds of kilobases in length. Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have pioneered competitive long read platforms, with more recent work focused on improving sequencing throughput and per-base accuracy. We used whole-genome sequencing data produced by three PacBio protocols (Sequel II CLR, Sequel II HiFi, RS II) and two ONT protocols (Rapid Sequencing and Ligation Sequencing) to compare assemblies of the bacteria Escherichia coli and the fruit fly Drosophila ananassae. In both organisms tested, Sequel II assemblies had the highest consensus accuracy, even after accounting for differences in sequencing throughput. ONT and PacBio CLR had the longest reads sequenced compared to PacBio RS II and HiFi, and genome contiguity was highest when assembling these datasets. ONT Rapid Sequencing libraries had the fewest chimeric reads in addition to superior quantification of E. coli plasmids versus ligation-based libraries. The quality of assemblies can be enhanced by adopting hybrid approaches using Illumina libraries for bacterial genome assembly or polishing eukaryotic genome assemblies, and an ONT-Illumina hybrid approach would be more cost-effective for many users. Genome-wide DNA methylation could be detected using both technologies, however ONT libraries enabled the identification of a broader range of known E. coli methyltransferase recognition motifs in addition to undocumented D. ananassae motifs. The ideal choice of long read technology may depend on several factors including the question or hypothesis under examination. No single technology outperformed others in all metrics examined. © The Author(s) 2021.
    Rights/Terms
    © The Author(s) (2021). Published by Oxford University Press on the Genetics Society of America.
    Keyword
    Drosophila ananassae
    bacterial genomics
    fly genomics
    genomics
    sequencing
    Identifier to cite or link to this item
    http://hdl.handle.net/10713/16343
    ae974a485f413a2113503eed53cd6c53
    10.1093/g3journal/jkab083
    Scopus Count
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