An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes

Perez-Sepulveda, Blanca M., Heavens, Darren, Pulford, Caisey V., Predeus, Alexander V., Low, Ross, Dykes, Gregory F., Schudoma, Christian, Rowe, Will, Lipscombe, James, Watkins, Chris, Shearer, Neil, Costigan, Karl, Baker, Kate S., Feasey, Nicholas A., Hinton, Jay C. D., Hall, Neil and , The 10KSG consortium (2021) An accessible, efficient and global approach for the large-scale sequencing of bacterial genomes. Genome Biology, 22 (1). ISSN 1474-760X

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Abstract

We have developed an efficient and inexpensive pipeline for streamlining large-scale collection and genome sequencing of bacterial isolates. Evaluation of this method involved a worldwide research collaboration focused on the model organism Salmonella enterica, the 10KSG consortium. Following the optimization of a logistics pipeline that involved shipping isolates as thermolysates in ambient conditions, the project assembled a diverse collection of 10,419 isolates from low- and middle-income countries. The genomes were sequenced using the LITE pipeline for library construction, with a total reagent cost of less than USD$10 per genome. Our method can be applied to other large bacterial collections to underpin global collaborations.

Item Type: Article
Additional Information: Funding Information: The project was supported by both a Global Challenges Research Fund (GCRF) data & resources grant BBS/OS/GC/000009D and the BBSRC Core Capability Grant to the Earlham Institute BB/CCG1720/1 and Core Strategic Programme Grant BBS/E/T/000PR9817. This project was partly supported by the Wellcome Trust Senior Investigator Award (106914/Z/15/Z) to Jay C. D. Hinton.
Uncontrolled Keywords: salmonella,thermolysates,whole-genome sequencing,ints,ecology, evolution, behavior and systematics,genetics,cell biology ,/dk/atira/pure/subjectarea/asjc/1100/1105
Faculty \ School: Faculty of Science > School of Biological Sciences
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Depositing User: LivePure Connector
Date Deposited: 23 Dec 2021 16:30
Last Modified: 20 Apr 2022 00:24
URI: https://ueaeprints.uea.ac.uk/id/eprint/82818
DOI: 10.1186/s13059-021-02536-3

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