A world of opportunities with nanopore sequencing

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

MinION as part of a biomedical rapidly deployable laboratory

(2017) Mathias C. Walter et al.   JOURNAL OF BIOTECHNOLOGY

Establishment and cryptic transmission of Zika virus in Brazil and the Americas

(2017) N. R. Faria et al.   NATURE

Detecting DNA cytosine methylation using nanopore sequencing

(2017) Jared T Simpson et al.   NATURE METHODS

Mapping DNA methylation with high-throughput nanopore sequencing

(2017) Arthur C Rand et al.   NATURE METHODS

Scaffolding and completing genome assemblies in real-time with nanopore sequencing

(2017) Minh Duc Cao et al.   Nature Communications

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

(2017) Vladimír Boža et al.   PLoS One

Evaluation of hybrid and non-hybrid methods forde novoassembly of nanopore reads

(2016) Ivan Sović et al.   BIOINFORMATICS

Nanocall: an open source basecaller for Oxford Nanopore sequencing data

(2016) Matei David et al.   BIOINFORMATICS

Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences

(2016) Heng Li   BIOINFORMATICS

Nanopore sequencing detects structural variants in cancer

(2016) Alexis L. Norris et al.   CANCER BIOLOGY & THERAPY

Identification of bacterial pathogens and antimicrobial resistance directly from clinical urines by nanopore-based metagenomic sequencing

(2016) K. Schmidt et al.   JOURNAL OF ANTIMICROBIAL CHEMOTHERAPY

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

(2016) Jane F. Turton et al.   JOURNAL OF MEDICAL MICROBIOLOGY

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

Real-time selective sequencing using nanopore technology

(2016) Matthew Loose et al.   NATURE METHODS

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

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

(2016) Minh Duc Cao et al.   GigaScience

Oxford Nanopore MinION Sequencing and Genome Assembly

(2016) Hengyun Lu et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

(2016) Timokratis Karamitros et al.   PLoS One

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

(2016) Stéphane Deschamps et al.   Scientific Reports

Integrated solid-state nanopore platform for nanopore fabrication via dielectric breakdown, DNA-speed deceleration and noise reduction

(2016) Yusuke Goto et al.   Scientific Reports

Analysis of nanopore data using hidden Markov models

(2015) Jacob Schreiber et al.   BIOINFORMATICS

Genome assembly using Nanopore-guided long and error-free DNA reads

(2015) Mohammed-Amin Madoui et al.   BMC GENOMICS

Noninvasive Prenatal Testing by Nanopore Sequencing of Maternal Plasma DNA: Feasibility Assessment

(2015) S. H. Cheng et al.   CLINICAL CHEMISTRY

Rapid Short-Read Sequencing and Aneuploidy Detection Using MinION Nanopore Technology

(2015) S. Wei et al.   GENETICS

Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome

(2015) Sara Goodwin et al.   GENOME RESEARCH

De novo sequencing and variant calling with nanopores using PoreSeq

(2015) Tamas Szalay et al.   NATURE BIOTECHNOLOGY

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

(2015) Nicholas J Loman et al.   NATURE METHODS

Improved data analysis for the MinION nanopore sequencer

(2015) Miten Jain et al.   NATURE METHODS

Rapid antibiotic-resistance predictions from genome sequence data for Staphylococcus aureus and Mycobacterium tuberculosis

(2015) Phelim Bradley et al.   Nature Communications

Scaffolding of a bacterial genome using MinION nanopore sequencing

(2015) E. Karlsson et al.   Scientific Reports

Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis

(2015) Alexander L. Greninger et al.   Genome Medicine

LINKS: Scalable, alignment-free scaffolding of draft genomes with long reads

(2015) René L. Warren et al.   GigaScience

poRe: an R package for the visualization and analysis of nanopore sequencing data

(2014) Mick Watson et al.   BIOINFORMATICS

Poretools: a toolkit for analyzing nanopore sequence data

(2014) N. J. Loman et al.   BIOINFORMATICS

Entering the era of bacterial epigenomics with single molecule real time DNA sequencing

(2013) Brigid M Davis et al.   CURRENT OPINION IN MICROBIOLOGY

Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data

(2013) Chen-Shan Chin et al.   NATURE METHODS

Detection and mapping of 5-methylcytosine and 5-hydroxymethylcytosine with nanopore MspA

(2013) A. H. Laszlo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error rates for nanopore discrimination among cytosine, methylcytosine, and hydroxymethylcytosine along individual DNA strands

(2013) J. Schreiber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory

(2012) Mark J Chaisson et al.   BMC BIOINFORMATICS

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Adaptive seeds tame genomic sequence comparison

(2011) S. M. Kielbasa et al.   GENOME RESEARCH

A flexible and efficient template format for circular consensus sequencing and SNP detection

(2010) K. J. Travers et al.   NUCLEIC ACIDS RESEARCH

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS