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Comparison of bacterial genome assembly software for MinION data

Kim Judge, Martin Hunt, Sandra Reuter, Alan Tracey, Michael A. Quail, Julian Parkhill, Sharon J. Peacock
doi: https://doi.org/10.1101/049213
Kim Judge
1University of Cambridge, Department of Medicine, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 OQQ, United Kingdom
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  • For correspondence: kj273@medschl.cam.ac.uk
Martin Hunt
2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Sandra Reuter
1University of Cambridge, Department of Medicine, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 OQQ, United Kingdom
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Alan Tracey
2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Michael A. Quail
2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Julian Parkhill
2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
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Sharon J. Peacock
1University of Cambridge, Department of Medicine, Box 157 Addenbrooke's Hospital, Hills Road, Cambridge, CB2 OQQ, United Kingdom
2Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
3University College London, Cruciform Building, London WC1E 6BT, United Kingdom
4London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
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Abstract

Antimicrobial resistance genes can be carried on plasmids or on mobile elements integrated into the chromosome. We sequenced a multidrug resistant Enterobacter kobei genome isolated from wastewater in the United Kingdom, but were unable to conclusively identify plasmids from the short read assembly. Our aim was to compare and contrast the accuracy and characteristics of open source software (PBcR, Canu, miniasm and SPAdes) for the assembly of bacterial genomes (including plasmids) generated by the MinION instrument. Miniasm produced an assembly in the shortest time, but Canu produced the most accurate assembly overall. We found that MinION data alone was able to generate a contiguous and accurate assembly of an isolate with multiple plasmids.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted May 24, 2016.
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Comparison of bacterial genome assembly software for MinION data
Kim Judge, Martin Hunt, Sandra Reuter, Alan Tracey, Michael A. Quail, Julian Parkhill, Sharon J. Peacock
bioRxiv 049213; doi: https://doi.org/10.1101/049213
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Comparison of bacterial genome assembly software for MinION data
Kim Judge, Martin Hunt, Sandra Reuter, Alan Tracey, Michael A. Quail, Julian Parkhill, Sharon J. Peacock
bioRxiv 049213; doi: https://doi.org/10.1101/049213

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