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Evaluation of Oxford nanopore’s MinION: Use, functionality, and genome assembly
Högskolan i Skövde, Institutionen för biovetenskap.
2019 (engelsk)Independent thesis Advanced level (degree of Master (Two Years)), 30 poäng / 45 hpOppgave
Abstract [en]

The rapid and reliable detection of pathogens is of utmost importance in healthcare settings to ensure the appropriate treatment thereby reducing morbidity and mortality for the patient. Current culturing, PCR based and NGS species detection methods are time consuming (Opota et al., 2015), limited in their detection (Buckley et al., 2015), or require specialist skills and are expensive (Basho and Eterovic., 2015). Oxford Technologies Nanopore devices could provide detailed genomic sequencing at a fraction of the cost and without the need for technical bioinformatic skills. This study evaluates the MinION device and analysis tools to suggest best practice. Classification and genotyping of 12 Klebsiella isolates were performed using EPI2ME automated workflows and manual de novo assembly.  Automated workflows using raw MinION reads provided clinically relevant information identified in ~6hrs. Manual de novo assembly and analysis used hybrid, and single source data took >24hrs. The inclusion of MinION long reads overcome problems assembling short reads. Hybrid genomes provided the most contiguous and highly detailed contigs. MinION only read assemblies contained more errors but still identified similar genotypic findings. Automated workflows are rapid and require minimal bioinformatic know-how. There should be a dialogue between clinicians and bioinformaticians to develop bespoke analysis tools.  Although challenges remain around compatible kits and vulnerable flowcells long read sequencing can be an effective tool for species detection and pathogen typing. Furthermore, hybrid assemblies have the potential to advance our genome detailing and discovery.

sted, utgiver, år, opplag, sider
2019. , s. 57
Emneord [en]
MinION, Genome, Klebsiella, NGS
HSV kategori
Identifikatorer
URN: urn:nbn:se:his:diva-17367OAI: oai:DiVA.org:his-17367DiVA, id: diva2:1334252
Fag / kurs
Systems Biology
Utdanningsprogram
Molecular Biotechnology - Master's Programme, 120 ECTS
Presentation
2019-06-05, 13:00 (engelsk)
Veileder
Examiner
Tilgjengelig fra: 2019-07-03 Laget: 2019-07-02 Sist oppdatert: 2019-07-03bibliografisk kontrollert

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