Research graph
References from Nanopore sequencing and its application to the study of microbial communities. Local targets link to admitted publications; unresolved targets remain external evidence.
Rapid determination of 16S ribosomal RNA sequences for phylogenetic analyses
10.1073/pnas.82.20.6955 · 1985 · External reference
10.1007/978-1-4757-0611-6_1
10.1007/978-1-4757-0611-6_1 · External reference
10.1038/nature08821
10.1038/nature08821 · External reference
10.1038/nature14486
10.1038/nature14486 · External reference
The Oxford Nanopore MinION: delivery of nanopore sequencing to the genomics community
10.1186/s13059-016-1103-0 · 2016 · External reference
10.1016/j.gpb.2016.05.004
10.1016/j.gpb.2016.05.004 · External reference
10.1093/bioinformatics/bty841
10.1093/bioinformatics/bty841 · External reference
10.1093/jxb/erx289
10.1093/jxb/erx289 · External reference
10.1038/nmeth.3444
10.1038/nmeth.3444 · External reference
NanoSatellite: Accurate characterization of expanded tandem repeat length and sequence through whole genome long-read sequencing on PromethION
10.1186/s13059-019-1856-3 · 2019 · External reference
10.1038/s41587-019-0293-x
10.1038/s41587-019-0293-x · External reference
10.1038/nmeth.4189
10.1038/nmeth.4189 · External reference
Highly parallel direct RN A sequencing on an array of nanopores
10.1038/nmeth.4577 · 2018 · External reference
10.1186/s13059-018-1462-9
10.1186/s13059-018-1462-9 · External reference
Unresolved reference
External reference
The vocabulary of microbiome research: a proposal
10.1186/s40168-015-0094-5 · 2015 · External reference
10.1128/cmr.17.4.840-862.2004
10.1128/cmr.17.4.840-862.2004 · External reference
10.1111/j.1469-0691.2008.02070.x
10.1111/j.1469-0691.2008.02070.x · External reference
10.1099/ijs.0.059774-0
10.1099/ijs.0.059774-0 · External reference
Current challenges and best-practice protocols for microbiome analysis
10.1093/bib/bbz155 · 2019 · External reference
Evaluation of 16S rRNA gene sequencing for species and strain-level microbiome analysis
10.1038/s41467-019-13036-1 · 2019 · External reference
Species-level resolution of 16S rRNA gene amplicons sequenced through the MinIONTM portable nanopore sequencer
10.1186/s13742-016-0111-z · 2016 · External reference
Analysis of the mouse gut microbiome using full-length 16S rRNA amplicon sequencing
10.1038/srep29681 · 2016 · External reference
A preliminary study on the potential of Nanopore MinION and Illumina MiSeq 16S rRNA gene sequencing to characterize building-dust microbiomes
10.1038/s41598-020-59771-0 · 2020 · External reference
NanoCLUST: a species-level analysis of 16S rRNA nanopore sequencing data
10.1101/2020.05.14.087353 · 2020 · External reference
10.1016/j.mimet.2018.09.015
10.1016/j.mimet.2018.09.015 · 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
10.1101/2020.05.06.078147
10.1101/2020.05.06.078147 · External reference
16S rRNA gene copy number normalization does not provide more reliable conclusions in metataxonomic surveys
10.1007/s00248-020-01586-7 · 2021 · External reference
10.1101/gr.5969107
10.1101/gr.5969107 · External reference
10.1038/s41587-019-0209-9
10.1038/s41587-019-0209-9 · External reference
10.1016/j.csbj.2020.01.005
10.1016/j.csbj.2020.01.005 · External reference
10.1093/bioinformatics/bty191
10.1093/bioinformatics/bty191 · External reference
10.1101/gr.210641.116
10.1101/gr.210641.116 · External reference
10.1186/s13059-019-1891-0
10.1186/s13059-019-1891-0 · 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
Real-time diagnostic analysis of MinIONTM-based metagenomic sequencing in clinical microbiology evaluation: a case report
10.1186/s40981-019-0244-z · 2019 · External reference
Rapid sequencing-based diagnosis of infectious bacterial species from meningitis patients in Zambia
10.1002/cti2.1087 · 2019 · External reference
A sample-to-report solution for taxonomic identification of cultured bacteria in the clinical setting based on nanopore sequencing
10.1128/jcm.00060-20 · 2020 · External reference
10.1038/nbt.3935
10.1038/nbt.3935 · External reference
10.1146/annurev.genet.38.072902.091216
10.1146/annurev.genet.38.072902.091216 · External reference
10.1016/j.tim.2009.11.003
10.1016/j.tim.2009.11.003 · External reference
Complete, closed bacterial genomes from microbiomes using nanopore sequencing
10.1038/s41587-020-0422-6 · 2020 · External reference
10.1038/nbt.3103
10.1038/nbt.3103 · External reference
Completing bacterial genome assemblies with multiplex MinION sequencing
2017 · External reference
Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology
10.1099/mgen.0.000085 · 2016 · External reference
10.1099/mgen.0.000118
10.1099/mgen.0.000118 · External reference
Complete genome sequences of bordetella pertussis clinical isolate FR5810 and reference strain tohama from combined oxford nanopore and illumina sequencing
10.1128/mra.01207-18 · 2018 · External reference
Improved high-molecular-weight DNA extraction, nanopore sequencing and metagenomic assembly from the human gut microbiome
10.1038/s41596-020-00424-x · 2021 · External reference
Unresolved reference
External reference
10.1038/nrmicro.2017.122
10.1038/nrmicro.2017.122 · External reference
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection
10.1038/s41587-019-0156-5 · 2019 · External reference
Benchmarking the MinION: evaluating long reads for microbial profiling
10.1038/s41598-020-61989-x · 2020 · External reference
10.1038/s10038-019-0659-4
10.1038/s10038-019-0659-4 · External reference
A comprehensive evaluation of long read error correction methods
10.1186/s12864-020-07227-0 · 2020 · External reference
A comparative evaluation of hybrid error correction methods for error-prone long reads
2019 · External reference
Benchmarking long-read assemblers for genomic analyses of bacterial pathogens using oxford nanopore sequencing
10.3390/ijms21239161 · 2020 · External reference
10.1016/s0022-2836(05)80360-2
10.1016/s0022-2836(05)80360-2 · External reference
High speed BLASTN: an accelerated MegaBLAST search tool
10.1093/nar/gkv784 · 2015 · External reference
MEGAN-LR: new algorithms allow accurate binning and easy interactive exploration of metagenomic long reads and contigs
10.1186/s13062-018-0208-7 · 2018 · External reference
10.1101/gr.113985.110
10.1101/gr.113985.110 · External reference
Halcyon: an accurate basecaller exploiting an encoder–decoder model with monotonic attention
2020 · External reference
Pair consensus decoding improves accuracy of neural network basecallers for nanopore sequencing
10.1186/s13059-020-02255-1 · 2021 · External reference
10.1186/gb-2014-15-3-r46
10.1186/gb-2014-15-3-r46 · External reference
10.1186/s13059-018-1568-0
10.1186/s13059-018-1568-0 · External reference
10.7717/peerj-cs.104
10.7717/peerj-cs.104 · External reference
10.1093/bioinformatics/btp324
10.1093/bioinformatics/btp324 · External reference
Bowtie2
2013 · External reference
Strain-level metagenomic assignment and compositional estimation for long reads with MetaMaps
10.1038/s41467-019-10934-2 · 2019 · External reference
10.1101/2020.02.08.939843
10.1101/2020.02.08.939843 · External reference
NanoSPC: a scalable, portable, cloud compatible viral nanopore metagenomic data processing pipeline
10.1093/nar/gkaa413 · 2020 · External reference
Mash: fast genome and metagenome distance estimation using MinHash
10.1186/s13059-016-0997-x · 2016 · External reference
10.1093/bioinformatics/btw152
10.1093/bioinformatics/btw152 · External reference
10.1101/gr.213959.116
10.1101/gr.213959.116 · External reference
10.1093/nar/gkx1068
10.1093/nar/gkx1068 · External reference
GenBank
10.1093/nar/gks1195 · 2013 · External reference
10.1128/aem.03006-05
10.1128/aem.03006-05 · External reference
10.1093/nar/gks1219
10.1093/nar/gks1219 · External reference
10.1093/nar/gkt1244
10.1093/nar/gkt1244 · External reference
10.1093/bioinformatics/btu153
10.1093/bioinformatics/btu153 · External reference
10.1093/nar/gkaa970
10.1093/nar/gkaa970 · External reference
10.1093/nar/gkz935
10.1093/nar/gkz935 · External reference
MEGARes: An antimicrobial resistance database for high throughput sequencing
10.1093/nar/gkw1009 · 2017 · External reference
RefSeq database growth influences the accuracy of k-mer-based lowest common ancestor species identification
10.1186/s13059-018-1554-6 · 2018 · External reference
Duplicates, redundancies and inconsistencies in the primary nucleotide databases: A descriptive study
10.1093/database/baw163 · 2017 · External reference
10.1038/nbt.2942
10.1038/nbt.2942 · External reference
DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data
10.1186/s40168-018-0401-z · 2018 · External reference
10.1093/gigascience/giz043
10.1093/gigascience/giz043 · External reference
10.1016/j.isci.2020.101223
10.1016/j.isci.2020.101223 · External reference
10.1101/gr.215087.116
10.1101/gr.215087.116 · External reference
10.1038/s41592-019-0669-3
10.1038/s41592-019-0669-3 · External reference
10.1101/2020.08.07.242461
10.1101/2020.08.07.242461 · External reference
10.1038/s41587-019-0202-3
10.1038/s41587-019-0202-3 · External reference
Assembly methods for nanopore-based metagenomic sequencing: a comparative study
10.1038/s41598-020-70491-3 · 2020 · External reference
10.1038/s41587-019-0191-2
10.1038/s41587-019-0191-2 · External reference
10.1038/s41592-020-00971-x
10.1038/s41592-020-00971-x · External reference
10.1038/s41564-019-0626-z
10.1038/s41564-019-0626-z · External reference
Rapid inference of antibiotic resistance and susceptibility by genomic neighbour typing
10.1038/s41564-019-0656-6 · 2020 · External reference
10.1038/s41591-020-0894-4
10.1038/s41591-020-0894-4 · External reference
10.1038/s41586-019-1065-y
10.1038/s41586-019-1065-y · External reference
10.1101/gr.251686.119
10.1101/gr.251686.119 · External reference
Accurate detection of m6A RNA modifications in native RNA sequences
2019 · External reference
10.1038/ncomms16027
10.1038/ncomms16027 · External reference
Multiple long-read sequencing survey of herpes simplex virus dynamic transcriptome
10.3389/fgene.2019.00834 · 2019 · External reference
10.1101/2019.12.13.876037
10.1101/2019.12.13.876037 · External reference
10.1093/gigascience/giaa002
10.1093/gigascience/giaa002 · External reference
Reading canonical and modified nucleobases in 16S ribosomal RNA using nanopore native RNA sequencing
10.1371/journal.pone.0216709 · 2019 · External reference
Direct RNA sequencing of the coding complete influenza a virus genome
2018 · External reference
10.1007/978-1-4939-3369-3_13
10.1007/978-1-4939-3369-3_13 · External reference
10.1016/j.marenvres.2019.104836
10.1016/j.marenvres.2019.104836 · External reference
10.1111/1755-0998.12399
10.1111/1755-0998.12399 · External reference
Magic-BLAST, an accurate RNA-seq aligner for long and short reads
10.1186/s12859-019-2996-x · 2019 · External reference
Blast2GO: A comprehensive suite for functional analysis in plant genomics
10.1155/2008/619832 · 2008 · External reference
10.1093/nar/gkw1092
10.1093/nar/gkw1092 · External reference
GoekeLab/bambu: bambu release version 0.3.0 (Version v0.3.0)
2020 · External reference
De novo clustering of long-read transcriptome data using a greedy, quality value-based algorithm
10.1089/cmb.2019.0299 · 2020 · External reference
Direct metatranscriptome RNA-seq and multiplex RT-PCR amplicon sequencing on nanopore MinION – promising strategies for multiplex identification of viable pathogens in food
2020 · External reference
10.2807/1560-7917.es.2018.23.50.1800228
10.2807/1560-7917.es.2018.23.50.1800228 · External reference
10.1038/nature16996
10.1038/nature16996 · External reference
10.1038/nprot.2017.066
10.1038/nprot.2017.066 · External reference
10.1056/nejmoa2001017
10.1056/nejmoa2001017 · External reference
10.17504/protocols.io.bp2l6n26rgqe/v3
10.17504/protocols.io.bp2l6n26rgqe/v3 · External reference
Rapid and inexpensive whole-genome sequencing of SARS-CoV-2 using 1200 bp tiled amplicons and oxford nanopore rapid barcoding
10.1093/biomethods/bpaa014 · 2020 · External reference
Coast-to-Coast Spread of SARS-CoV-2 during the Early Epidemic in the United States
10.1016/j.cell.2020.04.021 · 2020 · External reference
10.1016/s1473-3099(20)30562-4
10.1016/s1473-3099(20)30562-4 · External reference
Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis
10.1101/gr.247064.118 · 2019 · External reference
10.1016/j.cell.2020.04.011
10.1016/j.cell.2020.04.011 · External reference
10.1101/2020.03.05.976167
10.1101/2020.03.05.976167 · External reference
10.1128/mmbr.00016-06
10.1128/mmbr.00016-06 · External reference
10.1038/s41576-018-0081-3
10.1038/s41576-018-0081-3 · External reference
Detecting DNA cytosine methylation using nanopore sequencing
10.1038/nmeth.4184 · 2017 · External reference
10.1101/094672
10.1101/094672 · External reference
Single-molecule sequencing detection of N6-methyladenine in microbial reference materials
2019 · External reference
10.1093/bioinformatics/btz276
10.1093/bioinformatics/btz276 · External reference
Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data
10.1038/s41467-019-10168-2 · 2019 · External reference
10.1186/s13059-020-1935-5
10.1186/s13059-020-1935-5 · External reference
10.1101/2020.02.18.954636
10.1101/2020.02.18.954636 · External reference
Could lung bacterial dysbiosis predict ICU mortality in patients with extra-pulmonary sepsis? A proof-of-concept study
10.1007/s00134-020-06190-4 · 2020 · External reference
10.1101/2020.09.11.292896
10.1101/2020.09.11.292896 · External reference
10.1186/s13059-019-1727-y
10.1186/s13059-019-1727-y · External reference
High quality genome assemblies of Mycoplasma bovis using a taxon-specific Bonito basecaller for MinION and Flongle long-read nanopore sequencing
10.1186/s12859-020-03856-0 · 2020 · External reference
Real-time selective sequencing using nanopore technology
10.1038/nmeth.3930 · 2016 · External reference
Targeted nanopore sequencing by real-time mapping of raw electrical signal with UNCALLED
2020 · External reference
10.1101/2021.01.15.426907
10.1101/2021.01.15.426907 · External reference
Rapid resistome mapping using nanopore sequencing
2017 · External reference
