Shotgun metagenome data of a defined mock community using Oxford Nanopore, PacBio and Illumina technologies

[1]  T. Michael,et al.  Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies. , 2018, The Plant journal : for cell and molecular biology.

[2]  Richard E. Green,et al.  Improving nanopore read accuracy with the R2C2 method enables the sequencing of highly multiplexed full-length single-cell cDNA , 2018, Proceedings of the National Academy of Sciences.

[3]  M. Huss,et al.  Stationary and portable sequencing-based approaches for tracing wastewater contamination in urban stormwater systems , 2018, Scientific Reports.

[4]  Jelle Matthijnssens,et al.  Nanopore sequencing as a revolutionary diagnostic tool for porcine viral enteric disease complexes identifies porcine kobuvirus as an important enteric virus , 2018, Scientific Reports.

[5]  Yutaka Suzuki,et al.  Nanopore sequencing of drug-resistance-associated genes in malaria parasites, Plasmodium falciparum , 2018, Scientific Reports.

[6]  Dieter Deforce,et al.  Nanopore sequencing technology: a new route for the fast detection of unauthorized GMO , 2018, Scientific Reports.

[7]  Aaron Pomerantz,et al.  Real-time DNA barcoding in a rainforest using nanopore sequencing: opportunities for rapid biodiversity assessments and local capacity building , 2018, GigaScience.

[8]  Mathias Vandenbogaert,et al.  Early MinION™ nanopore single-molecule sequencing technology enables the characterization of hepatitis B virus genetic complexity in clinical samples , 2018, PloS one.

[9]  John R Tyson,et al.  MinION-based long-read sequencing and assembly extends the Caenorhabditis elegans reference genome , 2018, Genome research.

[10]  A. Ameur,et al.  Single molecule real-time (SMRT) sequencing comes of age: applications and utilities for medical diagnostics , 2018, Nucleic acids research.

[11]  Brent S. Pedersen,et al.  Nanopore sequencing and assembly of a human genome with ultra-long reads , 2017, Nature Biotechnology.

[12]  Yi Chen,et al.  Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples , 2017, Applied and Environmental Microbiology.

[13]  Tong Zhang,et al.  MinION Nanopore Sequencing Enables Correlation between Resistome Phenotype and Genotype of Coliform Bacteria in Municipal Sewage , 2017, Front. Microbiol..

[14]  Brian Bushnell,et al.  BBMerge – Accurate paired shotgun read merging via overlap , 2017, PloS one.

[15]  John P. Dekker,et al.  Rapid Nanopore Sequencing of Plasmids and Resistance Gene Detection in Clinical Isolates , 2017, Journal of Clinical Microbiology.

[16]  M. Huynen,et al.  Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis , 2017, Clinical Microbiology Reviews.

[17]  Joe Parker,et al.  Field-based species identification of closely-related plants using real-time nanopore sequencing , 2017, Scientific Reports.

[18]  T. Imanishi,et al.  A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer , 2017, Scientific Reports.

[19]  Sumio Sugano,et al.  Serotyping dengue virus with isothermal amplification and a portable sequencer , 2017, Scientific Reports.

[20]  Philip D. Blood,et al.  Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software , 2017, Nature Methods.

[21]  H. Spaink,et al.  De novo whole-genome assembly of a wild type yeast isolate using nanopore sequencing , 2017, F1000Research.

[22]  Jinyang Zhao,et al.  Genome sequencing of the sweetpotato whitefly Bemisia tabaci MED/Q , 2017, GigaScience.

[23]  R. Franklin,et al.  MinION TM nanopore sequencing of environmental metagenomes: a synthetic approach , 2017 .

[24]  Michael Liem,et al.  Rapid de novo assembly of the European eel genome from nanopore sequencing reads , 2017, Scientific Reports.

[25]  Phelim Bradley,et al.  Same-Day Diagnostic and Surveillance Data for Tuberculosis via Whole-Genome Sequencing of Direct Respiratory Samples , 2016, Journal of Clinical Microbiology.

[26]  Michael R. Lindberg,et al.  A Comparison and Integration of MiSeq and MinION Platforms for Sequencing Single Source and Mixed Mitochondrial Genomes , 2016, PloS one.

[27]  Jan-Fang Cheng,et al.  Next generation sequencing data of a defined microbial mock community , 2016, Scientific Data.

[28]  S. Deschamps,et al.  Characterization, correction and de novo assembly of an Oxford Nanopore genomic dataset from Agrobacterium tumefaciens , 2016, Scientific Reports.

[29]  Yaniv Erlich,et al.  Using mobile sequencers in an academic classroom , 2016, eLife.

[30]  M. Esumi,et al.  Pitfalls of DNA Quantification Using DNA-Binding Fluorescent Dyes and Suggested Solutions , 2016, PloS one.

[31]  Asaf Levy,et al.  High-resolution phylogenetic microbial community profiling , 2016, The ISME Journal.

[32]  David A. Matthews,et al.  Real-time, portable genome sequencing for Ebola surveillance , 2016, Nature.

[33]  Niranjan Nagarajan,et al.  INC-Seq: accurate single molecule reads using nanopore sequencing , 2016, bioRxiv.

[34]  John F. Mulley,et al.  Assessing the utility of the Oxford Nanopore MinION for snake venom gland cDNA sequencing , 2015, PeerJ.

[35]  S. Tringe,et al.  Impact of library preparation protocols and template quantity on the metagenomic reconstruction of a mock microbial community , 2015, BMC Genomics.

[36]  David A. Eccles,et al.  MinION Analysis and Reference Consortium: Phase 1 data release and analysis , 2015, F1000Research.

[37]  Yunfan Fan,et al.  Nanopore sequencing detects structural variants in cancer , 2015, bioRxiv.

[38]  Heng Li,et al.  BFC: correcting Illumina sequencing errors , 2015, Bioinform..

[39]  Richard J. Hall,et al.  MinION nanopore sequencing of an influenza genome , 2015, Front. Microbiol..

[40]  Gkikas Magiorkinis,et al.  A novel method for the multiplexed target enrichment of MinION next generation sequencing libraries using PCR-generated baits , 2015, Nucleic acids research.

[41]  Julian Parkhill,et al.  Early insights into the potential of the Oxford Nanopore MinION for the detection of antimicrobial resistance genes , 2015, The Journal of antimicrobial chemotherapy.

[42]  Joshua Quick,et al.  Rapid draft sequencing and real-time nanopore sequencing in a hospital outbreak of Salmonella , 2015, Genome Biology.

[43]  Alvin T. Liem,et al.  Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer , 2015, GigaScience.

[44]  T Laver,et al.  Assessing the performance of the Oxford Nanopore Technologies MinION , 2015, Biomolecular detection and quantification.

[45]  P. Ashton,et al.  MinION nanopore sequencing identifies the position and structure of a bacterial antibiotic resistance island , 2014, Nature Biotechnology.

[46]  N. Loman,et al.  A complete bacterial genome assembled de novo using only nanopore sequencing data , 2015, Nature Methods.

[47]  Sara Goodwin,et al.  Oxford Nanopore sequencing, hybrid error correction, and de novo assembly of a eukaryotic genome , 2015, bioRxiv.

[48]  A. Mikheyev,et al.  A first look at the Oxford Nanopore MinION sequencer , 2014, Molecular ecology resources.

[49]  Aaron R. Quinlan,et al.  A reference bacterial genome dataset generated on the MinION™ portable single-molecule nanopore sequencer , 2014, bioRxiv.

[50]  A. Quinlan BEDTools: The Swiss‐Army Tool for Genome Feature Analysis , 2014, Current protocols in bioinformatics.

[51]  T. Metz,et al.  Phototrophic biofilm assembly in microbial-mat-derived unicyanobacterial consortia: model systems for the study of autotroph-heterotroph interactions , 2014, Front. Microbiol..

[52]  Xiaorong Wei,et al.  Global pattern of soil carbon losses due to the conversion of forests to agricultural land , 2014, Scientific Reports.

[53]  A. Bashir,et al.  Diversified Microbiota of Meconium Is Affected by Maternal Diabetes Status , 2013, PloS one.

[54]  Mauricio O. Carneiro,et al.  The advantages of SMRT sequencing , 2013, Genome Biology.

[55]  Alexey A. Gurevich,et al.  QUAST: quality assessment tool for genome assemblies , 2013, Bioinform..

[56]  Katherine H. Huang,et al.  A framework for human microbiome research , 2012, Nature.

[57]  Sergey I. Nikolenko,et al.  SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing , 2012, J. Comput. Biol..

[58]  Juliane C. Dohm,et al.  Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems , 2011, Genome Biology.

[59]  Nancy F. Hansen,et al.  Accurate Whole Human Genome Sequencing using Reversible Terminator Chemistry , 2008, Nature.

[60]  Juliane C. Dohm,et al.  Substantial biases in ultra-short read data sets from high-throughput DNA sequencing , 2008, Nucleic acids research.

[61]  Gabor T. Marth,et al.  Whole-genome sequencing and variant discovery in C. elegans , 2008, Nature Methods.

[62]  Akwasi A. Boateng,et al.  Switchgrass as a biofuels feedstock in the USA , 2006 .

[63]  S. Salzberg,et al.  Versatile and open software for comparing large genomes , 2004, Genome Biology.

[64]  D. Moore,et al.  Preparation and Analysis of DNA , 2002 .

[65]  D. Branton,et al.  Characterization of individual polynucleotide molecules using a membrane channel. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[66]  A. Hiraishi,et al.  Chloroflexus aggregans sp. nov., a filamentous phototrophic bacterium which forms dense cell aggregates by active gliding movement. , 1995, International journal of systematic bacteriology.