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References from Computational methods for 16S metabarcoding studies using Nanopore sequencing data. Local targets link to admitted publications; unresolved targets remain external evidence.
High-throughput metagenomic technologies for complex microbial community analysis: open and closed formats
10.1128/mbio.02288-14 · 2015 · External reference
Fundamental questions in biology
10.1371/journal.pbio.0040300 · 2006 · External reference
The bright side of microbial dark matter: Lessons learned from the uncultivated majority
10.1016/j.mib.2016.04.020 · 2016 · External reference
Gene conservation in Bacillus species. I. Conserved genetic and nucleic acid base sequence homologies
1965 · External reference
Phylogenetic structure of the prokaryotic domain: the primary kingdoms
1977 · External reference
Molecular Markers in Phylogenetic Studies-A Review
10.4172/2329-9002.1000131 · 2014 · External reference
A compilation of large subunit (23S and 23S-like) ribosomal RNA structures: 1993
1993 · External reference
Impact of 16S rRNA gene sequence analysis for identification of bacteria on clinical microbiology and infectious diseases
10.1128/cmr.17.4.840-862.2004 · 2004 · External reference
On the evolutionary descent of organisms and organelles: a global phylogeny based on a highly conserved structural core in small subunit ribosomal RNA
1984 · External reference
Strengths and limitations of 16S rRNA gene amplicon sequencing in revealing temporal microbial community dynamics
10.1371/journal.pone.0093827 · 2014 · External reference
16S rRNA gene sequencing for bacterial identification in the diagnostic laboratory: pluses, perils, and pitfalls
2007 · External reference
10.1126/science.276.5313.734
10.1126/science.276.5313.734 · External reference
The effect of 16s rRNA region choice on bacterial community metabarcoding results
2019 · External reference
Metagenomic 16S rDNA Illumina tags are a powerful alternative to amplicon sequencing to explore diversity and structure of microbial communities
10.1111/1462-2920.12250 · 2014 · External reference
Coming of age: Ten years of next-generation sequencing technologies
2016 · External reference
10.1038/nature11209
10.1038/nature11209 · External reference
Earth microbiome project and global systems biology
10.1128/msystems.00217-17 · 2018 · External reference
Genomic methods and microbiological technologies for profiling novel and extreme environments for the extreme microbiome project (XMP)
10.7171/jbt.17-2801-004 · 2017 · External reference
Metagenomic analyses: past and future trends
2011 · External reference
10.1038/nmeth.f.303
10.1038/nmeth.f.303 · External reference
Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities
2009 · External reference
10.1371/journal.pone.0061217
10.1371/journal.pone.0061217 · External reference
Single-molecule sequencing of an individual human genome
10.1038/nbt.1561 · 2009 · External reference
Real-time DNA sequencing from single polymerase molecules
2009 · External reference
A tale of three next generation sequencing platforms: comparison of Ion Torrent, Pacific Biosciences and Illumina MiSeq sequencers
2012 · External reference
Improved performance of the PacBio SMRT technology for 16S rDNA sequencing
2014 · External reference
Evaluation of 16S rRNA amplicon sequencing using two next-generation sequencing technologies for phylogenetic analysis of the rumen bacterial community in steers
2016 · External reference
The Oxford Nanopore MinION: Delivery of nanopore sequencing to the genomics community
2016 · External reference
Three decades of nanopore sequencing
2016 · External reference
The Third Revolution in Sequencing Technology
10.1016/j.tig.2018.05.008 · 2018 · External reference
Nanopore-based fourth-generation DNA sequencing technology
10.1016/j.gpb.2016.01.001 · 2015 · External reference
Nanopore sequencing: review of potential applications in functional genomics
2019 · External reference
Improved data analysis for the MinION nanopore sequencer
2015 · External reference
DNA sequencing with nanopores
10.1038/nbt.2181 · 2012 · External reference
A review of the potential of the MinIONTM single-molecule sequencing system for forensic applications
10.1002/wfs2.1323 · 2019 · External reference
Newly designed 16S rRNA metabarcoding primers amplify diverse and novel archaeal taxa from the environment
2018 · External reference
PrimerProspector: De novo design and taxonomic analysis of barcoded polymerase chain reaction primers
10.1093/bioinformatics/btr087 · 2011 · External reference
Profiling bacterial communities by MinION sequencing of ribosomal operons
10.1186/s40168-017-0336-9 · 2017 · External reference
The madness of microbiome: attempting to find consensus “best practice” for 16S microbiome studies
10.1128/aem.02627-17 · 2018 · External reference
Experimental and analytical tools for studying the human microbiome
10.1038/nrg3129 · 2012 · External reference
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
10.1111/nph.14776 · 2018 · External reference
The bioinformatics tools for the genome assembly and analysis based on third-generation sequencing
2018 · External reference
Evaluation of Oxford Nanopore’s MinION sequencing device for microbial whole genome sequencing applications
2018 · External reference
Illumina and Nanopore methods for whole genome sequencing of hepatitis B virus (HBV)
10.1038/s41598-019-43524-9 · 2019 · External reference
Long-read sequencing uncovers a complex transcriptome topology in varicella zoster virus
10.1101/399048 · 2018 · External reference
Complete genomic and transcriptional landscape analysis using third-generation sequencing: A case study of Saccharomyces cerevisiae CEN.PK113-7D
10.1093/nar/gky014 · 2018 · External reference
Evaluation and application of RNA-Seq by MinION
2019 · External reference
10.1101/167015
10.1101/167015 · External reference
Methanogenic community shifts during the transition from sewage mono-digestion to co-digestion of grass biomass
10.1016/j.biortech.2018.06.005 · 2018 · External reference
10.1101/099960
10.1101/099960 · External reference
10.1101/073965
10.1101/073965 · External reference
Rapid bacterial identification by direct PCR amplification of 16S rRNA genes using the MinIONTM nanopore sequencer
10.1002/2211-5463.12590 · 2019 · External reference
New invasive nemertean species (Cephalothrix Simula) in England with high levels of tetrodotoxin and a microbiome linked to toxin metabolism
10.3390/md16110452 · 2018 · External reference
10.1093/bioinformatics/bty191
10.1093/bioinformatics/bty191 · External reference
10.7717/peerj.2584
10.7717/peerj.2584 · External reference
10.1093/nar/gkt1244
10.1093/nar/gkt1244 · External reference
A portable system for rapid bacterial composition analysis using a nanopore-based sequencer and laptop computer
10.1038/s41598-017-05772-5 · 2017 · External reference
10.1101/gr.210641.116
10.1101/gr.210641.116 · External reference
Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis
10.1186/s13073-015-0220-9 · 2015 · External reference
Nanopore sequencing data analysis: state of the art, applications and challenges
2018 · External reference
Characterization of MinION nanopore data for resequencing analyses
2017 · External reference
Offline next generation metagenomics sequence analysis using MinION detection Software (MINDS)
10.3390/genes10080578 · 2019 · External reference
Analysis of sequencing strategies and tools for taxonomic annotation: defining standards for progressive metagenomics
10.1038/s41598-018-30515-5 · 2018 · External reference
SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare?
10.1186/s12864-017-3501-4 · 2017 · External reference
10.1093/nar/gks1219
10.1093/nar/gks1219 · External reference
An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea
10.1038/ismej.2011.139 · 2012 · External reference
The NCBI taxonomy database
10.1093/nar/gkr1178 · 2012 · External reference
10.5808/gi.2018.16.4.e24
10.5808/gi.2018.16.4.e24 · External reference
Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies
2017 · External reference
High-throughput amplicon sequencing of the full-length 16S rRNA gene with single-nucleotide resolution
2019 · External reference
Species-level bacterial community profiling of the healthy sinonasal microbiome using Pacific Biosciences sequencing of full-length 16S rRNA genes 06 Biological Sciences 0604 Genetics 06 Biological Sciences 0605 Microbiology
2018 · External reference
Next-generation sequencing technologies and their application to the study and control of bacterial infections
2018 · External reference
Denoising PCR-amplified metagenome data
2012 · External reference
Piercing the dark matter: Bioinformatics of long-range sequencing and mapping
10.1038/s41576-018-0003-4 · 2018 · External reference
Search and clustering orders of magnitude faster than BLAST
10.1093/bioinformatics/btq461 · 2010 · External reference
10.1093/bioinformatics/btl158
10.1093/bioinformatics/btl158 · External reference
DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads
10.1371/journal.pone.0178751 · 2017 · External reference
10.1093/gigascience/giy037
10.1093/gigascience/giy037 · External reference
Performance of neural network basecalling tools for Oxford Nanopore sequencing
2019 · External reference
De novo clustering of long reads by gene from transcriptomics data
2018 · External reference
10.1093/gigascience/giy140
10.1093/gigascience/giy140 · External reference
10.1093/bioinformatics/bty149
10.1093/bioinformatics/bty149 · External reference
poRe: an R package for the visualization and analysis of nanopore sequencing data
2014 · External reference
Poretools: a toolkit for analyzing nanopore sequence data
10.1093/bioinformatics/btu555 · 2014 · External reference
Pavian: Interactive analysis of metagenomics data for microbiomics and pathogen identification
2016 · External reference
Phinch: An interactive, exploratory data visualization framework for –Omic datasets
2014 · External reference
Interactive metagenomic visualization in a Web browser
10.1186/1471-2105-12-385 · 2011 · External reference
Community edition - interactive exploration and analysis of large-scale microbiome sequencing
10.1371/journal.pcbi.1004957 · 2016 · External reference
MicrobiomeAnalyst: a web-based tool for comprehensive statistical, visual and meta-analysis of microbiome data
10.1093/nar/gkx295 · 2017 · External reference
10.1111/2041-210x.12613
10.1111/2041-210x.12613 · External reference
Unresolved reference
External reference
Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale
10.1093/gigascience/giz006 · 2019 · External reference
