Nanopore sequencing: Review of potential applications in functional genomics

NanoPipe—a web server for nanopore MinION sequencing data analysis

(2019) Victoria Shabardina et al.   GigaScience

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

npInv: accurate detection and genotyping of inversions using long read sub-alignment

(2018) Haojing Shao et al.   BMC BIOINFORMATICS

Draft genome of a high value tropical timber tree, Teak (Tectona grandis L. f): insights into SSR diversity, phylogeny and conservation

(2018) Ramasamy Yasodha et al.   DNA RESEARCH

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

(2018) Miten Jain et al.   NATURE BIOTECHNOLOGY

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

Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum

(2018) Lucky R. Runtuwene et al.   Scientific Reports

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

(2018) Haotian Teng et al.   GigaScience

Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies

(2018) Phuong N.T. Hoang et al.   PLANT JOURNAL

Single-Molecule Sequencing: Towards Clinical Applications

(2018) Adam Ameur et al.   TRENDS IN BIOTECHNOLOGY

BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files

(2018) Alexander Payne et al.   BIOINFORMATICS

Long-Read Annotation: Automated Eukaryotic Genome Annotation Based on Long-Read cDNA Sequencing

(2018) David E. Cook et al.   PLANT PHYSIOLOGY

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

The Nephila clavipes genome highlights the diversity of spider silk genes and their complex expression

(2017) Paul L Babb et al.   NATURE GENETICS

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

Multiplex PCR method for MinION and Illumina sequencing of Zika and other virus genomes directly from clinical samples

(2017) Joshua Quick et al.   Nature Protocols

Nanopore long-read RNAseq reveals widespread transcriptional variation among the surface receptors of individual B cells

(2017) Ashley Byrne et al.   Nature Communications

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

(2017) Mircea Cretu Stancu et al.   Nature Communications

Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy

(2017) Satomi Mitsuhashi et al.   Scientific Reports

Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads

(2017) Ryan R. Wick et al.   PLoS Computational Biology

de novo assembly and population genomic survey of natural yeast isolates with the Oxford Nanopore MinION sequencer

(2017) Benjamin Istace et al.   GigaScience

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

(2017) Vladimír Boža et al.   PLoS One

Serotyping dengue virus with isothermal amplification and a portable sequencer

(2017) Junya Yamagishi et al.   Scientific Reports

De novo yeast genome assemblies from MinION, PacBio and MiSeq platforms

(2017) Francesca Giordano et al.   Scientific Reports

A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer

(2017) Satomi Mitsuhashi et al.   Scientific Reports

Rapid de novo assembly of the European eel genome from nanopore sequencing reads

(2017) Hans J. Jansen et al.   Scientific Reports

Nanopore DNA Sequencing and Genome Assembly on the International Space Station

(2017) Sarah L. Castro-Wallace et al.   Scientific Reports

The 2016 World Health Organization Classification of Tumors of the Central Nervous System: a summary

(2016) David N. Louis et al.   ACTA NEUROPATHOLOGICA

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

The sequence of sequencers: The history of sequencing DNA

(2016) James M. Heather et al.   GENOMICS

Real-time, portable genome sequencing for Ebola surveillance

(2016) Joshua Quick et al.   NATURE

Nanopore development at Oxford Nanopore

(2016) Clive G Brown et al.   NATURE BIOTECHNOLOGY

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

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Assembly of long error-prone reads using de Bruijn graphs

(2016) Yu Lin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mobile real-time surveillance of Zika virus in Brazil

(2016) Nuno Rodrigues Faria et al.   Genome Medicine

Oxford Nanopore MinION Sequencing and Genome Assembly

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

DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies

(2016) Chengxi Ye et al.   Scientific Reports

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

Electrophoretic Deformation of Individual Transfer RNA Molecules Reveals Their Identity

(2015) Robert Y. Henley et al.   NANO LETTERS

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

(2015) Nicholas J Loman et al.   NATURE METHODS

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

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

Nanopore-based Fourth-generation DNA Sequencing Technology

(2015) Yanxiao Feng et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Structural and mechanistic insights into the bacterial amyloid secretion channel CsgG

(2014) Parveen Goyal et al.   NATURE

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

(2014) Philip M Ashton et al.   NATURE BIOTECHNOLOGY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Next-Generation Sequencing Platforms

(2013) Elaine R. Mardis   Annual Review of Analytical Chemistry

The MaSuRCA genome assembler

(2013) Aleksey V. Zimin et al.   BIOINFORMATICS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The limitations of draft assemblies for understanding prokaryotic adaptation and evolution

(2012) N. Ricker et al.   GENOMICS

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

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

Full-Length Minor Ampullate Spidroin Gene Sequence

(2012) Gefei Chen et al.   PLoS One

Adaptive seeds tame genomic sequence comparison

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

A window into third-generation sequencing

(2010) E. E. Schadt et al.   HUMAN MOLECULAR GENETICS

New Opportunities for an Ancient Material

(2010) F. G. Omenetto et al.   SCIENCE

Continuous base identification for single-molecule nanopore DNA sequencing

(2009) James Clarke et al.   Nature Nanotechnology

Aggressive assembly of pyrosequencing reads with mates

(2008) Jason R. Miller et al.   BIOINFORMATICS

The potential and challenges of nanopore sequencing

(2008) Daniel Branton et al.   NATURE BIOTECHNOLOGY

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE