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dc.contributor.authorTvedte, Eric S
dc.contributor.authorGasser, Mark
dc.contributor.authorSparklin, Benjamin C
dc.contributor.authorMichalski, Jane
dc.contributor.authorHjelmen, Carl E
dc.contributor.authorJohnston, J Spencer
dc.contributor.authorZhao, Xuechu
dc.contributor.authorBromley, Robin
dc.contributor.authorTallon, Luke J
dc.contributor.authorSadzewicz, Lisa
dc.contributor.authorRasko, David A
dc.contributor.authorDunning Hotopp, Julie Cen_US
dc.date.accessioned2021-08-09T14:06:42Z
dc.date.available2021-08-09T14:06:42Z
dc.date.issued2021-04-19
dc.identifier.urihttp://hdl.handle.net/10713/16343
dc.description.abstractThe 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.en_US
dc.description.urihttps://doi.org/10.1093/g3journal/jkab083en_US
dc.language.isoenen_US
dc.publisherOxford University Pressen_US
dc.relation.ispartofG3: Genes, Genomes, Geneticsen_US
dc.rights© The Author(s) (2021). Published by Oxford University Press on the Genetics Society of America.en_US
dc.subjectDrosophila ananassaeen_US
dc.subjectbacterial genomicsen_US
dc.subjectfly genomicsen_US
dc.subjectgenomicsen_US
dc.subjectsequencingen_US
dc.titleComparison of long read sequencing technologies in interrogating bacteria and fly genomesen_US
dc.typeArticleen_US
dc.identifier.doi10.1093/g3journal/jkab083
dc.identifier.pmid33768248
dc.source.countryEngland


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