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A single chromosome assembly of Bacteroides fragilis strain BE1 from Illumina and MinION nanopore sequencing data

Second and third generation sequencing technologies have revolutionised bacterial genomics. Short-read Illumina reads result in cheap but fragmented assemblies, whereas longer reads are more expensive but result in more complete genomes.

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What’s in my pot? Real-time species identification on the MinION

Whole genome sequencing on next-generation instruments provides an unbiased way to identify the organisms present in complex metagenomic samples. However, the time-to-result can be protracted because of fixed-time sequencing runs and cumbersome bioinformatics workflows.

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New Zealand Herald on MinION for mitochondrial genomes and pathogen monitoring

The New Zealand Herald interviews David Eccles on his work using MinION: “The device has been specifically used by the institute to sequence and com

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MinION in space

We are delighted that the MinION is scheduled to visit the International Space Station; this article from NASA explains what the project aims to achie

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MinION sequencing of malaria parasites

The MinION device by Oxford Nanopore is the first portable sequencing device. MinION is able to produce very long reads (reads over 100~kBp were reported), however it suffers from high sequencing error rate.

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Nanopore sequencing for metagenomic diagnosis of infectious diseases

Unbiased diagnosis of all pathogens in a single test by metagenomic next-generation sequencing is now feasible, but has been limited to date by concerns regarding sensitivity and sample-to-answer turnaround times.

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ZiBRA project: real-time sequencing of Zika virus in Brazil

A revolution is occurring in genomic epidemiology. Recently, real-time portable genome sequencing using the Oxford Nanopore MinION device was successfully used to characterize the genetic diversity of the Ebola virus outbreak in Guinea.

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Sequencers for Soldiers: Battlefield Genomics

Claire Lonsdale from the Defence Science and Technology Laboratory talks to the Nanopore community at London Calling 2016.

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A novel approach to elucidate the genomic structure of plants and pathogens

Alexander Wittenberg from KeyGene gives a talk at London Calling 2016.

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Applications of Nanopore Sequencing for Infectious Disease Detection

A talk by Stephanie Hao of Johns Hopkins University Applications of Nanopore Sequencing for Infectious Disease Detection at London Calling 2016.

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The Mystery of the Pink Lake

London Calling talk: The eXtreme Microbiome Project (XMP) Presents: The Mystery of the Pink Lake | Ken McGrath, Australian Genome Research Facility.

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How MinION is Changing my Research in Infectious Diseases Diagnostics

A presentation to the MinION Community by Dr Justin O’Grady, Lecturer in Medical Microbiology, University of East Anglia.

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Getting the Flu: Exploring Influenza Virus Evolutionary Dynamics by Single Molecule Sequencing

Elodie Ghedin - Professor of Biology and member of the Center for Genomics and Systems Biology, New York University - talks to the MinION community.

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NGS for Public Health Microbiology

Dr Catherine Arnold, Consultant Clinical Scientist in Molecular Microbiology at Public Health England talks to the MinION Community about NGS for Public Health Microbiology.

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Real-time Genomic Characterization of Viral Threat Agents using Nanopore Sequencing

Dr Andrew Kilianski presents a talk for the MinION Community on Real-time Genomic Characterization of Viral Threat Agents using Nanopore Sequencing.

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Applications of Long-read Sequencing in Infectious Disease Genomics

Next generation sequencing technology has revolutionised the study of microbial genomics, but most large-scale studies have focused on short-read sequencing. This use of short-read sequencing has limitations however.

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Nanopore sequencing – disruptive technology in clinical microbiology?

The diagnosis of infectious diseases by culture takes at least two days: one to grow the bacteria and then, at best, one to identify pathogens and test their antimicrobial susceptibility. Meanwhile the patient is treated empirically, which often results in inappropriate treatment.

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Whole genome sequencing of influenza virus genomes using MinION

A presentation by Nicole Moore at London Calling 2015.

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Real-time identification of pathogens and antibiotic resistance profile using Oxford Nanopore sequencing

Clinical pathogen sequencing has been demonstrated to have a positive outcome on treatment of patients with unknown bacterial infection. However, widespread adoption of clinical pathogen sequencing has been impeded by the lack of real-time sequencing devices.

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Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens

The MinION is a portable single-molecule DNA sequencing instrument that was released by Oxford Nanopore Technologies in 2014, producing long sequencing reads by measuring changes in ionic flow when single-stranded DNA molecules translocate through the pores.

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De Novo Assembly of Human Herpes Virus Type 1 (HHV-1) Genome, Mining of Non-Canonical Structures and Detection of Novel Drug-Resistance Mutations Using Short- and Long-Read Next Generation Sequencing Technologies

Human herpesvirus type 1 (HHV-1) has a large double-stranded DNA genome of approximately 152 kbp that is structurally complex and GC-rich. This makes the assembly of HHV-1 whole genomes from short-read sequencing data technically challenging.

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Comparison of bacterial genome assembly software for MinION data

Antimicrobial resistance genes can be carried on plasmids or on mobile elements integrated into the chromosome.

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Centrifuge: rapid and sensitive classification of metagenomic sequences

Centrifuge is a novel microbial classification engine that enables rapid, accurate and sensitive labeling of reads and quantification of species on desktop computers.

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Use of Unamplified RNA/cDNA–Hybrid Nanopore Sequencing for Rapid Detection and Characterization of RNA Viruses

Nanopore sequencing, a novel genomics technology, has potential applications for routine biosurveillance, clinical diagnosis, and outbreak investigation of virus infections.

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Enrichment of long DNA fragments from mixed samples for Nanopore sequencing

Whole-genome sequencing of pathogenic organisms directly from clinical samples combines detection and genotyping in one step.

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Clonal expansion of Escherichia coli ST38 carrying chromosomally-integrated OXA-48 carbapenemase gene

Many isolates of Escherichia coli carrying blaOXA-48 referred to Public Health England’s national reference laboratory during 2014 and 2015 shared similar pulsed-field gel electrophoresis (PFGE) profiles, despite coming from patients in multiple hospitals and regions.

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Real-time, portable genome sequencing for Ebola surveillance.

The Ebola virus disease epidemic in West Africa is the largest on record, responsible for over 28,599 cases and more than 11,299 deaths. Genome sequencing in viral outbreaks is desirable to characterise the infectious agent and determine its evolutionary rate.

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Species level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer

Background: The miniaturised and portable DNA sequencer MinION has been released to the scientific community within the framework of an early access programme to evaluate its application for a wide variety of genetic approaches.

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INC-Seq: Accurate single molecule reads using nanopore sequencing

Nanopore sequencing provides a rapid, cheap and portable real-time sequencing platform with the potential to revolutionise genomics. Several applications, including RNA-seq, haplotype sequencing and 16S sequencing, are however limited by its relatively high single read error rate (>10%).

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Rapid antibiotic resistance predictions from genome sequence data for S. aureus and M. tuberculosis

Rapid and accurate detection of antibiotic resistance in pathogens is an urgent need, affecting both patient care and population-scale control. Microbial genome sequencing promises much, but many barriers exist to its routine deployment.

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Nanopore Sequencing as a Rapidly Deployable Ebola Outbreak Tool

Rapid sequencing of RNA/DNA from pathogen samples obtained during disease outbreaks provides critical scientific and public health information. However, challenges exist for exporting samples to laboratories or establishing conventional sequencers in remote outbreak regions.

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Streaming algorithms for identification of pathogens and antibiotic resistance potential from real-time MinION sequencing

The recently introduced Oxford Nanopore MinION platform generates DNA sequence data in real-time. This opens immense potential to shorten the sample-to-results time and is likely to lead to enormous benefits in rapid diagnosis of bacterial infection and identification of drug resistance.

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Draft Genome Sequence of the Pandoraea apista LMG 16407 Type Strain

Pandoraea species, in particular Pandoraea apista, are opportunistic, multidrug-resistant pathogens in persons with cystic fibrosis (CF).

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MinION™ allied with 3D printed iChip – a workflow designed to let anyone discover new bacterial species in days

In this study, we adapt a protocol for the growth of previously uncultured environmental bacterial isolates, to make it compatible with whole genome sequencing.

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Real-time digital pathogen surveillance — the time is now

It is time to shake up public health surveillance. New technologies for sequencing, aided by friction-free approaches to data sharing, could have an impact on public health efforts.

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Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes

Genome sequencing will be increasingly used in the clinical setting to tailor antimicrobial prescribing and inform infection control outbreaks. A recent technological innovation that could reduce the delay between pathogen sampling and data generation is single molecule sequencing.

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A complete bacterial genome assembled de novo using only nanopore sequencing data

We have assembled de novo the Escherichia coli K-12 MG1655 chromosome in a single 4.6-Mb contig using only nanopore data.

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Nanopore sequencing of ebola viruses under outbreak conditions

Determining the full-length genome sequences of viruses during disease outbreaks such as the ongoing Ebola virus outbreak in West Africa, which is of unprecedented scale with about 24,000 cases and 10,000 deaths as of March 2015, can provide important information about virus evolution, and ensure

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An epidemiological river metagenome based on MinION

River waters worldwide are impacted by disease-causing agents including bacteria, protists, flatworms, viruses, and harmful algae that derive from domestic sewage and farm runoff, and/or are emergent due to nutrient pollution and climate change.

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Nanopore sequencing for genotyping pathogens of tropical diseases

Nanopore sequencer, MinION, has enabled sequencing analysis without pre-installation of expensive conventional sequencers or pre-requisite of specific skills in biological experiments. Even electric supply is not always necessary, by connecting MinION to a laptop PC.

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The MinION: Applications in Food safety (London Calling presentation)

Nanopore sequencing represents a paradigm shift in DNA sequencing, and today it is the only sequencing technology that measures an actual single molecule of DNA.

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Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer

The MinION™ nanopore sequencer was recently released to a community of alpha-testers for evaluation using a variety of sequencing applications.

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Assessing the performance of the Oxford Nanopore Technologies MinION

The Oxford Nanopore Technologies (ONT) MinION is a new sequencing technology that potentially offers read lengths of tens of kilobases (kb) limited only by the length of DNA molecules presented to it.

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MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island

Short-read, high-throughput sequencing technology cannot identify the chromosomal position of repetitive insertion sequences that typically flank horizontally acquired genes such as bacterial virulence genes and antibiotic resistance genes.

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