Real time, field-deployable whole genome sequencing of malaria parasites using nanopore technology

Razook, Z, Mehra, Somya, Gilchrist, B, Utama, D, Lautu-Gumal, D, Fola, A, Menard, D, Kazura, J, Laman, M, Mueller, I, Robinson, LJ, Bahlo, M and Barry, Alyssa 2020, Real time, field-deployable whole genome sequencing of malaria parasites using nanopore technology, bioRxiv (Preprints), pp. 1-43, doi: 10.1101/2020.12.17.423341.

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Title Real time, field-deployable whole genome sequencing of malaria parasites using nanopore technology
Author(s) Razook, Z
Mehra, Somya
Gilchrist, B
Utama, D
Lautu-Gumal, D
Fola, A
Menard, D
Kazura, J
Laman, M
Mueller, I
Robinson, LJ
Bahlo, MORCID iD for Bahlo, M orcid.org/0000-0002-1189-2310
Barry, Alyssa
Journal name bioRxiv (Preprints)
Start page 1
End page 43
Total pages 43
Publisher bioRxiv (Preprints)
Publication date 2020-12-21
Summary ABSTRACTMalaria parasite genomes have been generated predominantly using short read sequencing technology which can be slow, requires advanced laboratory training and does not adequately interrogate complex genomic regions that harbour important malaria virulence determinants. The portable Oxford Nanopore Technologies MinION platform generates long reads in real time and may overcome these limitations. We present compelling evidence that Nanopore sequencing delivers valuable additional information for malaria parasites with comparable data fidelity for single nucleotide variant (SNV) calls, compared to standard Illumina whole genome sequencing. We demonstrate this through sequencing of pure Plasmodium falciparum DNA, mock infections and natural isolates. Nanopore has low error rates for haploid SNV genotyping and identifies structural variants (SVs) not detected with short reads. Nanopore genomes are directly comparable to publically available genomes and produce high quality end to end chromosome assemblies. Nanopore sequencing will expedite genomic surveillance of malaria and provide new insights into parasite genome biology.
DOI 10.1101/2020.12.17.423341
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HERDC Research category C1 Refereed article in a scholarly journal
Persistent URL http://hdl.handle.net/10536/DRO/DU:30149565

Document type: Journal Article
Collections: Faculty of Health
School of Medicine
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