Nanopore sequencing technology, bioinformatics and applications

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

(2021) Søren M. Karst et al.   NATURE METHODS

S-conLSH: alignment-free gapped mapping of noisy long reads

(2021) Angana Chakraborty et al.   BMC BIOINFORMATICS

Comprehensive profiling of circular RNAs with nanopore sequencing and CIRI-long

(2021) Jinyang Zhang et al.   NATURE BIOTECHNOLOGY

Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm

(2021) Haoyu Cheng et al.   NATURE METHODS

Revealing nascent RNA processing dynamics with nano-COP

(2021) Heather L. Drexler et al.   Nature Protocols

DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples

(2021) Steffen Klasberg et al.   BMC BIOINFORMATICS

Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing

(2021) Oguzhan Begik et al.   NATURE BIOTECHNOLOGY

Nanopanel2 calls phased low-frequency variants in Nanopore panel sequencing data

(2021) Niko Popitsch et al.   BIOINFORMATICS

Accurate spliced alignment of long RNA sequencing reads

(2021) Kristoffer Sahlin et al.   BIOINFORMATICS

Nanopore sequencing of single-cell transcriptomes with scCOLOR-seq

(2021) Martin Philpott et al.   NATURE BIOTECHNOLOGY

Identification of differential RNA modifications from nanopore direct RNA sequencing with xPore

(2021) Ploy N. Pratanwanich et al.   NATURE BIOTECHNOLOGY

lra: A long read aligner for sequences and contigs

(2021) Jingwen Ren et al.   PLoS Computational Biology

Methplotlib: analysis of modified nucleotides from nanopore sequencing

(2020) Wouter De Coster et al.   BIOINFORMATICS

Long live the king: chromosome-level assembly of the lion (Panthera leo) using linked-read, Hi-C, and long-read data

(2020) Ellie E. Armstrong et al.   BMC BIOLOGY

The full-length transcriptome of C. elegans using direct RNA sequencing

(2020) Nathan P. Roach et al.   GENOME RESEARCH

Genomic characterisation and epidemiology of 2019 novel coronavirus: implications for virus origins and receptor binding

(2020) Roujian Lu et al.   LANCET

Targeted nanopore sequencing with Cas9-guided adapter ligation

(2020) Timothy Gilpatrick et al.   NATURE BIOTECHNOLOGY

Long-range single-molecule mapping of chromatin accessibility in eukaryotes

(2020) Zohar Shipony et al.   NATURE METHODS

DNA extraction of microbial DNA directly from infected tissue: an optimized protocol for use in nanopore sequencing

(2020) Karin Helmersen et al.   Scientific Reports

LongQC: A Quality Control Tool for Third Generation Sequencing Long Read Data

(2020) Yoshinori Fukasawa et al.   G3-Genes Genomes Genetics

Nanopore direct RNA sequencing maps the complexity of Arabidopsis mRNA processing and m6A modification

(2020) Matthew T Parker et al.   eLife

Causalcall: Nanopore Basecalling Using a Temporal Convolutional Network

(2020) Jingwen Zeng et al.   Frontiers in Genetics

DeepNano-blitz: A Fast Base Caller for MinION Nanopore Sequencers

(2020) Vladimír Boža et al.   BIOINFORMATICS

Nanopore basecalling from a perspective of instance segmentation

(2020) Yao-zhong Zhang et al.   BMC BIOINFORMATICS

De novo assembly of the olive fruit fly (Bactrocera oleae) genome with linked-reads and long-read technologies minimizes gaps and provides exceptional Y chromosome assembly

(2020) Anthony Bayega et al.   BMC GENOMICS

The Architecture of SARS-CoV-2 Transcriptome

(2020) Dongwan Kim et al.   CELL

Nanopore sequencing and the Shasta toolkit enable efficient de novo assembly of eleven human genomes

(2020) Kishwar Shafin et al.   NATURE BIOTECHNOLOGY

De Novo Genome Assembly of the Meadow Brown Butterfly, Maniola jurtina

(2020) Kumar Saurabh Singh et al.   G3-Genes Genomes Genetics

Nanopore Sequencing of a Forensic STR Multiplex Reveals Loci Suitable for Single-Contributor STR Profiling

(2020) Olivier Tytgat et al.   Genes

High-quality chromosome-scale assembly of the walnut (Juglans regia L.) reference genome

(2020) Annarita Marrano et al.   GigaScience

TALC: Transcript-level Aware Long Read Correction

(2020) Lucile Broseus et al.   BIOINFORMATICS

RabbitQC: High-speed scalable quality control for sequencing data

(2020) Zekun Yin et al.   BIOINFORMATICS

smsMap: mapping single molecule sequencing reads by locating the alignment starting positions

(2020) Ze-Gang Wei et al.   BMC BIOINFORMATICS

Telomere-to-telomere assembly of a complete human X chromosome

(2020) Karen H. Miga et al.   NATURE

Detection of base analogs incorporated during DNA replication by nanopore sequencing

(2020) Daniela Georgieva et al.   NUCLEIC ACIDS RESEARCH

Decoding the epitranscriptional landscape from native RNA sequences

(2020) Piroon Jenjaroenpun et al.   NUCLEIC ACIDS RESEARCH

Nanopore Targeted Sequencing for the Accurate and Comprehensive Detection of SARS‐CoV‐2 and Other Respiratory Viruses

(2020) Ming Wang et al.   Small

High throughput error corrected Nanopore single cell transcriptome sequencing

(2020) Kevin Lebrigand et al.   Nature Communications

The genome polishing tool POLCA makes fast and accurate corrections in genome assemblies

(2020) Aleksey V. Zimin et al.   PLoS Computational Biology

NanoReviser: An Error-Correction Tool for Nanopore Sequencing Based on a Deep Learning Algorithm

(2020) Luotong Wang et al.   Frontiers in Genetics

Implications of Error-Prone Long-Read Whole-Genome Shotgun Sequencing on Characterizing Reference Microbiomes

(2020) Yu Hu et al.   iScience

QAlign: Aligning nanopore reads accurately using current-level modeling

(2020) Dhaivat Joshi et al.   BIOINFORMATICS

Next-generation technologies applied to age-old challenges in Madagascar

(2020) Marina B. Blanco et al.   CONSERVATION GENETICS

Native molecule sequencing by nano-ID reveals synthesis and stability of RNA isoforms

(2020) Kerstin C. Maier et al.   GENOME RESEARCH

metaFlye: scalable long-read metagenome assembly using repeat graphs

(2020) Mikhail Kolmogorov et al.   NATURE METHODS

TRiCoLOR: tandem repeat profiling using whole-genome long-read sequencing data

(2020) Davide Bolognini et al.   GigaScience

Nanopore Sequencing Enables Comprehensive Transposable Element Epigenomic Profiling

(2020) Adam D. Ewing et al.   MOLECULAR CELL

Simultaneous profiling of chromatin accessibility and methylation on human cell lines with nanopore sequencing

(2020) Isac Lee et al.   NATURE METHODS

Direct RNA sequencing reveals m6A modifications on adenovirus RNA are necessary for efficient splicing

(2020) Alexander M. Price et al.   Nature Communications

SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism

(2020) Neng Huang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

SVIM: Structural Variant Identification using Mapped Long Reads

(2019) David Heller et al.   BIOINFORMATICS

Metagenomic sequencing at the epicenter of the Nigeria 2018 Lassa fever outbreak

(2019) L. E. Kafetzopoulou et al.   SCIENCE

Evaluation of the detection of GBA missense mutations and other variants using the Oxford Nanopore MinION

(2019) Melissa Leija-Salazar et al.   Molecular Genetics & Genomic Medicine

Epidemiologic and genomic insights on mcr-1-harbouring Salmonella from diarrhoeal outpatients in Shanghai, China, 2006–2016

(2019) Xin Lu et al.   EBioMedicine

Ultra-long Read Sequencing for Whole Genomic DNA Analysis

(2019) Liang Gong et al.   Jove-Journal of Visualized Experiments

Rapid Sequencing of Multiple RNA Viruses in Their Native Form

(2019) Thidathip Wongsurawat et al.   Frontiers in Microbiology

Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana

(2019) Steve Hamner et al.   International Journal of Environmental Research and Public Health

FLAS: fast and high throughput algorithm for PacBio long read self-correction

(2019) Ergude Bao et al.   BIOINFORMATICS

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning

(2019) Peng Ni et al.   BIOINFORMATICS

PyPore: a python toolbox for nanopore sequencing data handling

(2019) Roberto Semeraro et al.   BIOINFORMATICS

The Dark Matter of Large Cereal Genomes: Long Tandem Repeats

(2019) Veronika Kapustová et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Severe hemophilia A caused by an unbalanced chromosomal rearrangement identified using nanopore sequencing

(2019) Nicolas Chatron et al.   JOURNAL OF THROMBOSIS AND HAEMOSTASIS

Increasing the accuracy of nanopore DNA sequencing using a time-varying cross membrane voltage

(2019) Matthew T. Noakes et al.   NATURE BIOTECHNOLOGY

Assembly of long, error-prone reads using repeat graphs

(2019) Mikhail Kolmogorov et al.   NATURE BIOTECHNOLOGY

Capturing the dynamics of genome replication on individual ultra-long nanopore sequence reads

(2019) Carolin A. Müller et al.   NATURE METHODS

NanoR: A user-friendly R package to analyze and compare nanopore sequencing data

(2019) Davide Bolognini et al.   PLoS One

Long-read direct RNA sequencing by 5’-Cap capturing reveals the impact of Piwi on the widespread exonization of transposable elements in locusts

(2019) Feng Jiang et al.   RNA Biology

Sequencing of human genomes with nanopore technology

(2019) Rory Bowden et al.   Nature Communications

De novo assembly of the Indian blue peacock (Pavo cristatus) genome using Oxford Nanopore technology and Illumina sequencing

(2019) Ruby Dhar et al.   GigaScience

Ultra-deep, long-read nanopore sequencing of mock microbial community standards

(2019) Samuel M Nicholls et al.   GigaScience

Magic-BLAST, an accurate RNA-seq aligner for long and short reads

(2019) Grzegorz M. Boratyn et al.   BMC BIOINFORMATICS

Nanopore Sequencing Significantly Improves Genome Assembly of the Protozoan Parasite Trypanosoma cruzi

(2019) Florencia Díaz-Viraqué et al.   Genome Biology and Evolution

Structural variants identified by Oxford Nanopore PromethION sequencing of the human genome

(2019) Wouter De Coster et al.   GENOME RESEARCH

Single-molecule long-read sequencing reveals the chromatin basis of gene expression

(2019) Yunhao Wang et al.   GENOME RESEARCH

Resolving MiSeq-Generated Ambiguities in HLA-DPB1 Typing by Using the Oxford Nanopore Technology

(2019) Jamie L. Duke et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Hybrid metagenomic assembly enables high-resolution analysis of resistance determinants and mobile elements in human microbiomes

(2019) Denis Bertrand et al.   NATURE BIOTECHNOLOGY

Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

(2019) Themoula Charalampous et al.   NATURE BIOTECHNOLOGY

Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing

(2019) Andrew M. Smith et al.   PLoS One

A comprehensive examination of Nanopore native RNA sequencing for characterization of complex transcriptomes

(2019) Charlotte Soneson et al.   Nature Communications

The Genome of the Steller Sea Lion (Eumetopias jubatus)

(2019) Harwood H. Kwan et al.   Genes

Genome of the Komodo dragon reveals adaptations in the cardiovascular and chemosensory systems of monitor lizards

(2019) Abigail L. Lind et al.   Nature Ecology & Evolution

Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis

(2019) Adrian Viehweger et al.   GENOME RESEARCH

Rapid diagnosis of bacterial meningitis by nanopore 16S amplicon sequencing: A pilot study

(2019) Jangsup Moon et al.   INTERNATIONAL JOURNAL OF MEDICAL MICROBIOLOGY

Tree Lab: Portable genomics for Early Detection of Plant Viruses and Pests in Sub-Saharan Africa

(2019) Boykin et al.   Genes

Hybrid genome assembly and annotation of Danionella translucida

(2019) Mykola Kadobianskyi et al.   Scientific Data

Analysis of short tandem repeat expansions and their methylation state with nanopore sequencing

(2019) Pay Giesselmann et al.   NATURE BIOTECHNOLOGY

Nanopore native RNA sequencing of a human poly(A) transcriptome

(2019) Rachael E. Workman et al.   NATURE METHODS

Direct RNA sequencing enables m6A detection in endogenous transcript isoforms at base-specific resolution

(2019) Daniel A. Lorenz et al.   RNA

Longshot enables accurate variant calling in diploid genomes from single-molecule long read sequencing

(2019) Peter Edge et al.   Nature Communications

Rapid detection of chromosomal translocation and precise breakpoint characterization in acute myeloid leukemia by nanopore long-read sequencing

(2019) Chun Hang Au et al.   Cancer Genetics

Splicing Kinetics and Coordination Revealed by Direct Nascent RNA Sequencing through Nanopores

(2019) Heather L. Drexler et al.   MOLECULAR CELL

Fast and accurate long-read assembly with wtdbg2

(2019) Jue Ruan et al.   NATURE METHODS

Identification and characterization of occult human-specific LINE-1 insertions using long-read sequencing technology

(2019) Weichen Zhou et al.   NUCLEIC ACIDS RESEARCH

lordFAST: sensitive and Fast Alignment Search Tool for LOng noisy Read sequencing Data

(2018) Ehsan Haghshenas et al.   BIOINFORMATICS

IDP-denovo: de novo transcriptome assembly and isoform annotation by hybrid sequencing

(2018) Shuhua Fu et al.   BIOINFORMATICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Hybrid correction of highly noisy long reads using a variable-order de Bruijn graph

(2018) Pierre Morisse et al.   BIOINFORMATICS

NanoPack: visualizing and processing long-read sequencing data

(2018) Wouter De Coster et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

FMLRC: Hybrid long read error correction using an FM-index

(2018) Jeremy R. Wang et al.   BMC BIOINFORMATICS

Nanopore sequencing technology and tools for genome assembly: computational analysis of the current state, bottlenecks and future directions

(2018) Damla Senol Cali et al.   BRIEFINGS IN BIOINFORMATICS

Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital

(2018) Claire L Gorrie et al.   CLINICAL INFECTIOUS DISEASES

SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

(2018) Manuel Tardaguila et al.   GENOME RESEARCH

Breakpoint mapping of a novel de novo translocation t(X;20)(q11.1;p13) by positional cloning and long read sequencing

(2018) Usha R. Dutta et al.   GENOMICS

Accurate Typing of Human Leukocyte Antigen Class I Genes by Oxford Nanopore Sequencing

(2018) Chang Liu et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Nanopore sequencing and assembly of a human genome with ultra-long reads

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Linear assembly of a human centromere on the Y chromosome

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

Expansions of intronic TTTCA and TTTTA repeats in benign adult familial myoclonic epilepsy

(2018) Hiroyuki Ishiura et al.   NATURE GENETICS

Picky comprehensively detects high-resolution structural variants in nanopore long reads

(2018) Liang Gong et al.   NATURE METHODS

Highly parallel direct RNA sequencing on an array of nanopores

(2018) Daniel R Garalde et al.   NATURE METHODS

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

Selective nanopore sequencing of human BRCA1 by Cas9-assisted targeting of chromosome segments (CATCH)

(2018) Tslil Gabrieli et al.   NUCLEIC ACIDS RESEARCH

Acquisition of virulence genes by a carrier strain gave rise to the ongoing epidemics of meningococcal disease in West Africa

(2018) Ola Brønstad Brynildsrud et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Paternally inherited cis-regulatory structural variants are associated with autism

(2018) William M. Brandler et al.   SCIENCE

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Genomic BCR-ABL1 breakpoint characterization by a multi-strategy approach for “personalized monitoring” of residual disease in chronic myeloid leukemia patients

(2018) Cosimo Cumbo et al.   Oncotarget

Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning

(2018) Haotian Teng et al.   GigaScience

A fast adaptive algorithm for computing whole-genome homology maps

(2018) Chirag Jain et al.   BIOINFORMATICS

Real-time analysis of nanopore-based metagenomic sequencing from infected orthopaedic devices

(2018) Nicholas D Sanderson et al.   BMC GENOMICS

De novo assembly of middle-sized genome using MinION and Illumina sequencers

(2018) Ryuhei Minei et al.   BMC GENOMICS

Long-read sequencing identified intronic repeat expansions in SAMD12 from Chinese pedigrees affected with familial cortical myoclonic tremor with epilepsy

(2018) Sheng Zeng et al.   JOURNAL OF MEDICAL GENETICS

A nanopore sequencing–based assay for rapid detection of gene fusions

(2018) William R. Jeck et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

The axolotl genome and the evolution of key tissue formation regulators

(2018) Sergej Nowoshilow et al.   NATURE

De novo clustering of long reads by gene from transcriptomics data

(2018) Camille Marchet et al.   NUCLEIC ACIDS RESEARCH

Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA

(2018) Roger Volden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic and epidemiological monitoring of yellow fever virus transmission potential

(2018) N. R. Faria et al.   SCIENCE

Structural, Physiological and Regulatory Analysis of Maltose Transporter Genes in Saccharomyces eubayanus CBS 12357T

(2018) Anja Brickwedde et al.   Frontiers in Microbiology

Tracking microevolution events among ST11 carbapenemase-producing hypervirulent Klebsiella pneumoniae outbreak strains

(2018) Ning Dong et al.   Emerging Microbes & Infections

Long-read sequencing identified a causal structural variant in an exome-negative case and enabled preimplantation genetic diagnosis

(2018) Hefan Miao et al.   HEREDITAS

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Evaluation and application of RNA-Seq by MinION

(2018) Masahide Seki et al.   DNA RESEARCH

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

A chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping

(2018) Stéphane Deschamps et al.   Nature Communications

Identification of pathogens in culture-negative infective endocarditis cases by metagenomic analysis

(2018) Jun Cheng et al.   Annals of Clinical Microbiology and Antimicrobials

NanoAmpli-Seq: A workflow for amplicon sequencing for mixed microbial communities on the nanopore sequencing platform.

(2018) Szymon T Calus et al.   GigaScience

Mutational analysis in BCR - ABL1 positive leukemia by deep sequencing based on nanopore MinION technology

(2017) Crescenzio F. Minervini et al.   EXPERIMENTAL AND MOLECULAR PATHOLOGY

MinION-based long-read sequencing and assembly extends theCaenorhabditis elegansreference genome

(2017) John R. Tyson et al.   GENOME RESEARCH

Fast and accurate de novo genome assembly from long uncorrected reads

(2017) Robert Vaser et al.   GENOME RESEARCH

HINGE: long-read assembly achieves optimal repeat resolution

(2017) Govinda M. Kamath 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

A world of opportunities with nanopore sequencing

(2017) Richard M Leggett et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2017) N. R. Faria et al.   NATURE

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads

(2017) Chuan-Le Xiao et al.   NATURE METHODS

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

Mapping and phasing of structural variation in patient genomes using nanopore sequencing

(2017) Mircea Cretu Stancu et al.   Nature Communications

Rapid re-identification of human samples using portable DNA sequencing

(2017) Sophie Zaaijer et al.   eLife

De novo genome assembly and annotation of Australia's largest freshwater fish, the Murray cod (Maccullochella peelii), from Illumina and Nanopore sequencing read

(2017) Christopher M. Austin et al.   GigaScience

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

(2017) Vladimír Boža et al.   PLoS One

Jabba: hybrid error correction for long sequencing reads

(2016) Giles Miclotte et al.   Algorithms for Molecular Biology

Nanopore Sensing

(2016) Wenqing Shi et al.   ANALYTICAL CHEMISTRY

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

CoLoRMap: Correcting Long Reads by Mapping short reads

(2016) Ehsan Haghshenas et al.   BIOINFORMATICS

HPG pore: an efficient and scalable framework for nanopore sequencing data

(2016) Joaquin Tarraga et al.   BMC BIOINFORMATICS

Nanopore sequencing detects structural variants in cancer

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

TP53 gene mutation analysis in chronic lymphocytic leukemia by nanopore MinION sequencing

(2016) Crescenzio Francesco Minervini et al.   Diagnostic Pathology

HapCUT2: robust and accurate haplotype assembly for diverse sequencing technologies

(2016) Peter Edge et al.   GENOME RESEARCH

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

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

De novo assembly and phasing of a Korean human genome

(2016) Jeong-Sun Seo et al.   NATURE

Three decades of nanopore sequencing

(2016) David Deamer et al.   NATURE BIOTECHNOLOGY

Phased diploid genome assembly with single-molecule real-time sequencing

(2016) Chen-Shan Chin et al.   NATURE METHODS

IDP-ASE: haplotyping and quantifying allele-specific expression at the gene and gene isoform level by hybrid sequencing

(2016) Benjamin Deonovic et al.   NUCLEIC ACIDS RESEARCH

Fast and sensitive mapping of nanopore sequencing reads with GraphMap

(2016) Ivan Sović et al.   Nature Communications

cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing

(2016) Maria Cartolano et al.   PLoS One

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

(2016) Spyros Oikonomopoulos et al.   Scientific Reports

Realtime analysis and visualization of MinION sequencing data with npReader

(2015) Minh Duc Cao et al.   BIOINFORMATICS

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

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

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

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

(2015) Nicholas J Loman et al.   NATURE METHODS

Characterization of fusion genes and the significantly expressed fusion isoforms in breast cancer by hybrid sequencing

(2015) Jason L. Weirather et al.   NUCLEIC ACIDS RESEARCH

The evolution of nanopore sequencing

(2015) Yue Wang et al.   Frontiers in Genetics

PacBio Sequencing and Its Applications

(2015) Anthony Rhoads et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

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

proovread : large-scale high-accuracy PacBio correction through iterative short read consensus

(2014) Thomas Hackl et al.   BIOINFORMATICS

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

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Advances in Nanopore Sequencing Technology

(2013) Yongqiang Yang et al.   JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY

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

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Recent advances in nanopore sequencing

(2012) Raj D. Maitra et al.   ELECTROPHORESIS

Hybrid error correction and de novo assembly of single-molecule sequencing reads

(2012) Sergey Koren et al.   NATURE BIOTECHNOLOGY

Genome-wide mapping of methylated adenine residues in pathogenic Escherichia coli using single-molecule real-time sequencing

(2012) Gang Fang et al.   NATURE BIOTECHNOLOGY

Reading DNA at single-nucleotide resolution with a mutant MspA nanopore and phi29 DNA polymerase

(2012) Elizabeth A Manrao et al.   NATURE BIOTECHNOLOGY

Automated forward and reverse ratcheting of DNA in a nanopore at 5-Å precision

(2012) Gerald M Cherf et al.   NATURE BIOTECHNOLOGY

Improving PacBio Long Read Accuracy by Short Read Alignment

(2012) Kin Fai Au et al.   PLoS One

Faster sequencers, larger datasets, new challenges

(2012) Christopher E Mason et al.   GENOME BIOLOGY

The birth of the Epitranscriptome: deciphering the function of RNA modifications

(2012) Yogesh Saletore et al.   GENOME BIOLOGY

Adaptive seeds tame genomic sequence comparison

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

Processive Replication of Single DNA Molecules in a Nanopore Catalyzed by phi29 DNA Polymerase

(2010) Kate R. Lieberman et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Nucleobase Recognition in ssDNA at the Central Constriction of the α-Hemolysin Pore

(2010) David Stoddart et al.   NANO LETTERS

DNA Translocation through Graphene Nanopores

(2010) Christopher A. Merchant et al.   NANO LETTERS

DNA Translocation through Graphene Nanopores

(2010) Grégory F. Schneider et al.   NANO LETTERS

Graphene as a subnanometre trans-electrode membrane

(2010) S. Garaj et al.   NATURE

Nanopore DNA sequencing with MspA

(2010) I. M. Derrington et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiple Base-Recognition Sites in a Biological Nanopore: Two Heads are Better than One

(2009) David Stoddart et al.   ANGEWANDTE CHEMIE-INTERNATIONAL EDITION

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Single-molecule sequencing of an individual human genome

(2009) Dmitry Pushkarev et al.   NATURE BIOTECHNOLOGY

Single-nucleotide discrimination in immobilized DNA oligonucleotides with a biological nanopore

(2009) D. Stoddart et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Single-Molecule Nanopore Device Detects DNA Polymerase Activity with Single-Nucleotide Resolution

(2008) Scott L. Cockroft et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Single-molecule DNA detection with an engineered MspA protein nanopore

(2008) T. Z. Butler et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA