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Evaluation of a Nanopore Sequencing Strategy on Bacterial Communities From Marine Sediments

https://doi.org/10.1002/edn3.70009
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Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/ece3.8676openalex-snapshot
Effects of operational taxonomic unit inference methods on soil microeukaryote community analysis using long‐read metabarcoding
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The impact of intragenomic rRNA variation on metabarcoding‐derived diversity estimates: A case study from marine nematodes
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16S rRNA Gene Analysis with QIIME2
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Evaluation of Full-Length Versus V4-Region 16S rRNA Sequencing for Phylogenetic Analysis of Mouse Intestinal Microbiota After a Dietary Intervention
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Characterizing algal microbiomes using long-read nanopore sequencing
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Metagenomic tools in microbial ecology research
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Evaluation of bacterial consortia associated with dairy fermentation by ribosomal RNA (rrn) operon metabarcoding strategy using MinION device
inferredcites →https://doi.org/10.1016/j.foodcont.2022.109388openalex-snapshot
Evaluation of DNA metabarcoding using Oxford Nanopore sequencing for authentication of mixed seafood products
inferredcites →https://doi.org/10.1016/j.gpb.2016.05.004openalex-snapshot
Oxford Nanopore MinION Sequencing and Genome Assembly
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/nmicrobiol.2016.242openalex-snapshot
Relic DNA is abundant in soil and obscures estimates of soil microbial diversity
inferredcites →https://doi.org/10.1038/s41587-019-0156-5openalex-snapshot
Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection
inferredcites →https://doi.org/10.1038/s41592-020-01041-yopenalex-snapshot
High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing
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High throughput resistance profiling of Plasmodium falciparum infections based on custom dual indexing and Illumina next generation sequencing-technology
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Elucidation of the bacterial communities associated with the harmful microalgae Alexandrium tamarense and Cochlodinium polykrikoides using nanopore sequencing
inferredcites →https://doi.org/10.1038/s41598-018-29334-5openalex-snapshot
Evaluation of Oxford Nanopore’s MinION Sequencing Device for Microbial Whole Genome Sequencing Applications
inferredcites →https://doi.org/10.1038/s41598-020-74180-zopenalex-snapshot
Identification of plastic-associated species in the Mediterranean Sea using DNA metabarcoding with Nanopore MinION
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The effect of taxonomic classification by full-length 16S rRNA sequencing with a synthetic long-read technology
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A general framework for quantitatively assessing ecological stochasticity
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Properties of the Rarefaction Diversity Measurement
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NanoPack: visualizing and processing long-read sequencing data
inferredcites →https://doi.org/10.1093/femsec/fiab001openalex-snapshot
Is Oxford Nanopore sequencing ready for analyzing complex microbiomes?
inferredcites →https://doi.org/10.1093/femsec/fiac120openalex-snapshot
Co-occurrences enhance our understanding of aquatic fungal metacommunity assembly and reveal potential host–parasite interactions
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Influence of 16S rRNA variable region on perceived diversity of marine microbial communities of the Northern North Atlantic
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Species-level evaluation of the human respiratory microbiome
inferredcites →https://doi.org/10.1093/gigascience/gix007openalex-snapshot
MinION™ nanopore sequencing of environmental metagenomes: a synthetic approach
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
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R2C2 + UMI: Combining concatemeric and unique molecular identifier–based consensus sequencing enables ultra-accurate sequencing of amplicons on Oxford Nanopore Technologies sequencers
inferredcites →https://doi.org/10.1101/585067openalex-snapshot
Shallow metagenomics with Nanopore sequencing in canine fecal microbiota improved bacterial taxonomy and identified an uncultured CrAssphage
inferredcites →https://doi.org/10.1111/1462-2920.13023openalex-snapshot
Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples
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Long‐ and short‐read metabarcoding technologies reveal similar spatiotemporal structures in fungal communities
inferredcites →https://doi.org/10.1111/1755-0998.13610openalex-snapshot
Speeding up the detection of invasive bivalve species using environmental DNA: A Nanopore and Illumina sequencing comparison
inferredcites →https://doi.org/10.1111/2041-210x.13561openalex-snapshot
A workflow for accurate metabarcoding using nanopore MinION sequencing
inferredcites →https://doi.org/10.1111/j.1365-2656.2009.01525.xopenalex-snapshot
Undersampling bias: the null hypothesis for singleton species in tropical arthropod surveys
inferredcites →https://doi.org/10.1111/mec.16534openalex-snapshot
Nanopore sequencing of full rRNA operon improves resolution in mycobiome analysis and reveals high diversity in both human gut and environments
inferredcites →https://doi.org/10.1111/nph.14070openalex-snapshot
High‐resolution community profiling of arbuscular mycorrhizal fungi
inferredcites →https://doi.org/10.1111/nph.14776openalex-snapshot
PacBio metabarcoding of Fungi and other eukaryotes: errors, biases and perspectives
inferredcites →https://doi.org/10.1128/aem.00626-21openalex-snapshot
Perspectives and Benefits of High-Throughput Long-Read Sequencing in Microbial Ecology
inferredcites →https://doi.org/10.1128/aem.01368-19openalex-snapshot
Relative Performance of MinION (Oxford Nanopore Technologies) versus Sequel (Pacific Biosciences) Third-Generation Sequencing Instruments in Identification of Agricultural and Forest Fungal Pathogens
inferredcites →https://doi.org/10.1128/aem.02953-09openalex-snapshot
Diversity of 16S rRNA Genes within Individual Prokaryotic Genomes
inferredcites →https://doi.org/10.1128/jb.173.2.697-703.1991openalex-snapshot
16S ribosomal DNA amplification for phylogenetic study
inferredcites →https://doi.org/10.1128/msphere.01202-20openalex-snapshot
Primer, Pipelines, Parameters: Issues in 16S rRNA Gene Sequencing
inferredcites →https://doi.org/10.1128/msystems.00009-15openalex-snapshot
Improved Bacterial 16S rRNA Gene (V4 and V4-5) and Fungal Internal Transcribed Spacer Marker Gene Primers for Microbial Community Surveys
inferredcites →https://doi.org/10.1186/1471-2105-10-421openalex-snapshot
BLAST+: architecture and applications
inferredcites →https://doi.org/10.1186/s12866-021-02094-5openalex-snapshot
Full-length 16S rRNA gene amplicon analysis of human gut microbiota using MinION™ nanopore sequencing confers species-level resolution
inferredcites →https://doi.org/10.1186/s13742-016-0111-zopenalex-snapshot
Species-level resolution of 16S rRNA gene amplicons sequenced through the MinION™ portable nanopore sequencer
inferredcites →https://doi.org/10.1186/s40168-017-0396-xopenalex-snapshot
Combining 16S rRNA gene variable regions enables high-resolution microbial community profiling
inferredcites →https://doi.org/10.1371/journal.pone.0030087openalex-snapshot
Direct Comparisons of Illumina vs. Roche 454 Sequencing Technologies on the Same Microbial Community DNA Sample
inferredcites →https://doi.org/10.1371/journal.pone.0057923openalex-snapshot
The Variability of the 16S rRNA Gene in Bacterial Genomes and Its Consequences for Bacterial Community Analyses
inferredcites →https://doi.org/10.1371/journal.pone.0061217openalex-snapshot
phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data
inferredcites →https://doi.org/10.1371/journal.pone.0163962openalex-snapshot
SeqKit: A Cross-Platform and Ultrafast Toolkit for FASTA/Q File Manipulation
inferredcites →https://doi.org/10.1890/11-1952.1openalex-snapshot
Coverage‐based rarefaction and extrapolation: standardizing samples by completeness rather than size
inferredcites →https://doi.org/10.3390/genes10060468openalex-snapshot
A Rapid and Accurate MinION-Based Workflow for Tracking Species Biodiversity in the Field
inferredcites →https://doi.org/10.3390/genes11091105openalex-snapshot
Comparison of Illumina versus Nanopore 16S rRNA Gene Sequencing of the Human Nasal Microbiota
inferredcites →https://doi.org/10.3897/mycokeys.86.77431openalex-snapshot
A long-read amplicon approach to scaling up the metabarcoding of lichen herbarium specimens
inferredcites →https://doi.org/10.7554/elife.61504openalex-snapshot
Freshwater monitoring by nanopore sequencing

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.3897/mbmg.9.163750zenodo-depositor-declared
From short to long reads: enhanced protist diversity profiling via Nanopore metabarcoding
inferred← citeshttps://doi.org/10.1016/j.ecolind.2026.115637openalex-snapshot
Generalist taxa shape microbial community responses to riverine pollution and contribute to multi-element biogeochemical cycling
inferred← citeshttps://doi.org/10.1242/bio.062230openalex-snapshot
Taxonomic diversity and functional adaptations indicated by the rhizospheric soil microbiome derived from Turkish wheat fields
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