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A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding
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What this work says
Outgoing claims: the papers this work cites, builds on, or argues with.
inferredcites →https://doi.org/10.1002/ece3.1485openalex-snapshot
Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?
inferredcites →https://doi.org/10.1002/ece3.2667openalex-snapshot
Effect of marker choice and thermal cycling protocol on zooplankton DNA metabarcoding studies
inferredcites →https://doi.org/10.1002/ece3.4814openalex-snapshot
Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments
inferredcites →https://doi.org/10.1006/mpev.1999.0642openalex-snapshot
Miocene Radiation of Deep-Sea Hydrothermal Vent Shrimp (Caridea: Bresiliidae): Evidence from Mitochondrial Cytochrome Oxidase Subunit I
inferredcites →https://doi.org/10.1007/978-3-319-17001-5_53-1openalex-snapshot
Metabarcoding Techniques for Assessing Biodiversity of Marine Animal Forests
inferredcites →https://doi.org/10.1016/j.biocon.2014.11.018openalex-snapshot
Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA
inferredcites →https://doi.org/10.1016/j.margen.2015.04.010openalex-snapshot
Metagenetic tools for the census of marine meiofaunal biodiversity: An overview
inferredcites →https://doi.org/10.1016/j.margen.2015.05.007openalex-snapshot
Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods
inferredcites →https://doi.org/10.1016/j.soilbio.2016.01.008openalex-snapshot
Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA
inferredcites →https://doi.org/10.1016/j.ympev.2009.12.024openalex-snapshot
Phylogeny of the bristle worm family Eunicidae (Eunicida, Annelida) and the phylogenetic utility of noncongruent 16S, COI and 18S in combined analyses
inferredcites →https://doi.org/10.1016/s0169-5347(01)02151-6openalex-snapshot
Mitochondrial pseudogenes: evolution's misplaced witnesses
inferredcites →https://doi.org/10.1038/ismej.2015.137openalex-snapshot
Global diversity and biogeography of deep-sea pelagic prokaryotes
inferredcites →https://doi.org/10.1038/ismej.2017.119openalex-snapshot
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
inferredcites →https://doi.org/10.1038/ncomms1095openalex-snapshot
Second-generation environmental sequencing unmasks marine metazoan biodiversity
inferredcites →https://doi.org/10.1038/ncomms12544openalex-snapshot
Environmental DNA reveals that rivers are conveyer belts of biodiversity information
inferredcites →https://doi.org/10.1038/nmeth.2276openalex-snapshot
Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
inferredcites →https://doi.org/10.1038/nmeth.f.303openalex-snapshot
QIIME allows analysis of high-throughput community sequencing data
inferredcites →https://doi.org/10.1038/nrmicro1236openalex-snapshot
Re-evaluating prokaryotic species
inferredcites →https://doi.org/10.1038/s41467-017-01312-xopenalex-snapshot
Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates
inferredcites →https://doi.org/10.1038/s41598-017-12501-5openalex-snapshot
Ecosystem biomonitoring with eDNA: metabarcoding across the tree of life in a tropical marine environment
inferredcites →https://doi.org/10.1038/s41598-018-30157-7openalex-snapshot
Multi-marker metabarcoding approach to study mesozooplankton at basin scale
inferredcites →https://doi.org/10.1038/sdata.2017.27openalex-snapshot
Metazoan mitochondrial gene sequence reference datasets for taxonomic assignment of environmental samples
inferredcites →https://doi.org/10.1073/pnas.0502030102openalex-snapshot
Ernst Mayr and the modern concept of species
inferredcites →https://doi.org/10.1073/pnas.0803076105openalex-snapshot
Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified
inferredcites →https://doi.org/10.1073/pnas.1209160109openalex-snapshot
The widely used small subunit 18S rDNA molecule greatly underestimates true diversity in biodiversity surveys of the meiofauna
inferredcites →https://doi.org/10.1080/10635150118398openalex-snapshot
Bacterial Species and Speciation
inferredcites →https://doi.org/10.1086/282646openalex-snapshot
The Biological Species Concept: A Critical Evaluation
inferredcites →https://doi.org/10.1093/nar/29.1.181openalex-snapshot
rrndb: the Ribosomal RNA Operon Copy Number Database
inferredcites →https://doi.org/10.1093/nar/gks1219openalex-snapshot
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
inferredcites →https://doi.org/10.1093/oxfordjournals.molbev.a025643openalex-snapshot
Evidence that two types of 18S rDNA coexist in the genome of Dugesia (Schmidtea) mediterranea (Platyhelminthes, Turbellaria, Tricladida)
inferredcites →https://doi.org/10.1111/1462-2920.12955openalex-snapshot
Marine protist diversity in E uropean coastal waters and sediments as revealed by high‐throughput sequencing
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
inferredcites →https://doi.org/10.1111/1755-0998.12254openalex-snapshot
Performance comparison of genetic markers for high‐throughput sequencing‐based biodiversity assessment in complex communities
inferredcites →https://doi.org/10.1111/1755-0998.12338openalex-snapshot
Replication levels, false presences and the estimation of the presence/absence from eDNA metabarcoding data
inferredcites →https://doi.org/10.1111/1755-0998.12402openalex-snapshot
Tag jumps illuminated – reducing sequence‐to‐sample misidentifications in metabarcoding studies
inferredcites →https://doi.org/10.1111/1755-0998.12428openalex-snapshot
obitools : a unix ‐inspired software package for DNA metabarcoding
inferredcites →https://doi.org/10.1111/1755-0998.12433openalex-snapshot
Quantification of mesocosm fish and amphibian species diversity via environmental DNA metabarcoding
inferredcites →https://doi.org/10.1111/1755-0998.12895openalex-snapshot
Minimizing polymerase biases in metabarcoding
inferredcites →https://doi.org/10.1111/1755-0998.12902openalex-snapshot
“Pitfalls in relative abundance estimation using eDNA metabarcoding”
inferredcites →https://doi.org/10.1111/1755-0998.12922openalex-snapshot
Testing clustering strategies for metabarcoding‐based investigation of community–environment interactions
inferredcites →https://doi.org/10.1111/2041-210x.12574openalex-snapshot
The ecologist's field guide to sequence‐based identification of biodiversity
inferredcites →https://doi.org/10.1111/2041-210x.12595openalex-snapshot
Critical considerations for the application of environmental DNA methods to detect aquatic species
inferredcites →https://doi.org/10.1111/2041-210x.12849openalex-snapshot
Scrutinizing key steps for reliable metabarcoding of environmental samples
inferredcites →https://doi.org/10.1111/ele.12162openalex-snapshot
Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding
inferredcites →https://doi.org/10.1111/j.1365-294x.2009.04325.xopenalex-snapshot
Comparative phylogeography among hydrothermal vent species along the East Pacific Rise reveals vicariant processes and population expansion in the South
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05297.xopenalex-snapshot
Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep‐sea and shallow water sediments
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05545.xopenalex-snapshot
DNA from soil mirrors plant taxonomic and growth form diversity
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05550.xopenalex-snapshot
Bioinformatic challenges for DNA metabarcoding of plants and animals
inferredcites →https://doi.org/10.1111/j.2041-210x.2012.00198.xopenalex-snapshot
Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring
inferredcites →https://doi.org/10.1111/j.2041-210x.2012.00224.xopenalex-snapshot
betapart: an R package for the study of beta diversity
inferredcites →https://doi.org/10.1111/mec.12419openalex-snapshot
High connectivity across the fragmented chemosynthetic ecosystems of the deep A tlantic E quatorial B elt: efficient dispersal mechanisms or questionable endemism?
inferredcites →https://doi.org/10.1111/mec.13054openalex-snapshot
Evolutionary and biogeographical patterns of barnacles from deep‐sea hydrothermal vents
inferredcites →https://doi.org/10.1111/mec.13428openalex-snapshot
Next‐generation monitoring of aquatic biodiversity using environmental DNA metabarcoding
inferredcites →https://doi.org/10.1111/mec.14844openalex-snapshot
Why the COI barcode should be the community DNA metabarcode for the metazoa
inferredcites →https://doi.org/10.1126/sciadv.aap9661openalex-snapshot
Environmental DNA illuminates the dark diversity of sharks
inferredcites →https://doi.org/10.1126/science.1122033openalex-snapshot
Population Size Does Not Influence Mitochondrial Genetic Diversity in Animals
inferredcites →https://doi.org/10.1126/science.1261605openalex-snapshot
Eukaryotic plankton diversity in the sunlit ocean
inferredcites →https://doi.org/10.1126/science.aam9695openalex-snapshot
Neandertal and Denisovan DNA from Pleistocene sediments
inferredcites →https://doi.org/10.1128/aem.01541-09openalex-snapshot
Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities
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.185.3.966-972.2003openalex-snapshot
Rates and Consequences of Recombination between rRNA Operons
inferredcites →https://doi.org/10.1128/jb.186.9.2629-2635.2004openalex-snapshot
Divergence and Redundancy of 16S rRNA Sequences in Genomes with Multiple rrn Operons
inferredcites →https://doi.org/10.1139/gen-2015-0184openalex-snapshot
The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data
inferredcites →https://doi.org/10.1146/annurev-marine-120308-080950openalex-snapshot
DNA Barcoding of Marine Metazoa
inferredcites →https://doi.org/10.1186/1471-2180-10-189openalex-snapshot
ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases
inferredcites →https://doi.org/10.1186/1742-9994-10-34openalex-snapshot
A new versatile primer set targeting a short fragment of the mitochondrial COI region for metabarcoding metazoan diversity: application for characterizing coral reef fish gut contents
inferredcites →https://doi.org/10.1186/gb-2011-12-11-r112openalex-snapshot
Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and Genome Analyzer systems
inferredcites →https://doi.org/10.1186/s13742-015-0086-1openalex-snapshot
Evaluating a multigene environmental DNA approach for biodiversity assessment
inferredcites →https://doi.org/10.1186/s40168-018-0605-2openalex-snapshot
Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data
inferredcites →https://doi.org/10.1371/journal.pone.0013716openalex-snapshot
Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes
inferredcites →https://doi.org/10.1371/journal.pone.0018169openalex-snapshot
Eukaryotic Richness in the Abyss: Insights from Pyrotag Sequencing
inferredcites →https://doi.org/10.1371/journal.pone.0023398openalex-snapshot
Persistence of Environmental DNA in Freshwater Ecosystems
inferredcites →https://doi.org/10.1371/journal.pone.0035887openalex-snapshot
PCR Primers for Metazoan Mitochondrial 12S Ribosomal DNA Sequences
inferredcites →https://doi.org/10.1371/journal.pone.0046180openalex-snapshot
PCR Primers for Metazoan Nuclear 18S and 28S Ribosomal DNA Sequences
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.0066643openalex-snapshot
A Filtering Method to Generate High Quality Short Reads Using Illumina Paired-End Technology
inferredcites →https://doi.org/10.1371/journal.pone.0117562openalex-snapshot
Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3354/ame044097openalex-snapshot
Molecular detection of marine nematodes from environmental samples: overcoming eukaryotic interference
inferredcites →https://doi.org/10.3389/fmars.2016.00092openalex-snapshot
Worldwide Analysis of Sedimentary DNA Reveals Major Gaps in Taxonomic Knowledge of Deep-Sea Benthos
inferredcites →https://doi.org/10.7717/peerj.1420openalex-snapshot
Swarm v2: highly-scalable and high-resolution amplicon clustering
inferredcites →https://doi.org/10.7717/peerj.5364openalex-snapshot
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
What points at this work
Incoming claims: where this work appears in other papers’ reference lists and arguments.
inferred← citeshttps://doi.org/10.1002/edn3.561openalex-snapshot
Detecting the invisible through DNA metabarcoding: The role of gelatinous taxa in the diet of two demersal Antarctic key stone fish species (Notothenioidei)
inferred← citeshttps://doi.org/10.1038/s41598-021-86396-8openalex-snapshot
Evaluating sediment and water sampling methods for the estimation of deep-sea biodiversity using environmental DNA
inferred← citeshttps://doi.org/10.1101/2021.01.08.425760openalex-snapshot
To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
inferred← citeshttps://doi.org/10.1111/ibi.70046openalex-snapshot
Family templates and trophic filtering shape passerine gut microbiota with scale‐dependent phylosymbiosis
inferred← citeshttps://doi.org/10.1186/s12859-021-04115-6openalex-snapshot
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
inferred← citeshttps://doi.org/10.24072/pci.ecology.100043openalex-snapshot
A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding
inferred← citeshttps://doi.org/10.31390/gradschool_theses.5287openalex-snapshot
A Comparison of Intertidal Metazoan Biodiversity Between Previously Oiled Sheared and Intact Marsh Margins and Between Multiple Salinity Zones in the Coastal Marshes of Louisiana
inferred← citeshttps://doi.org/10.3389/fenvs.2022.950527openalex-snapshot
A comparison of intertidal metazoan biodiversity among different salinity zones of Louisiana coastal marshes
inferred← citeshttps://doi.org/10.3389/fmars.2019.00783openalex-snapshot
Exploring Environmental DNA (eDNA) to Assess Biodiversity of Hard Substratum Faunal Communities on the Lucky Strike Vent Field (Mid-Atlantic Ridge) and Investigate Recolonization Dynamics After an Induced Disturbance
inferred← citeshttps://doi.org/10.3389/fmars.2020.00234openalex-snapshot
An Assessment of Environmental Metabarcoding Protocols Aiming at Favoring Contemporary Biodiversity in Inventories of Deep-Sea Communities
inferred← citeshttps://doi.org/10.3389/fmars.2021.692538openalex-snapshot
A Beginner’s Guide on Integrating *Omics Approaches to Study Marine Microbial Communities: Details and Discussions From Sample Collection to Bioinformatics Analysis
inferred← citeshttps://doi.org/10.3389/fmars.2024.1423676openalex-snapshot
Detecting local variations across metazoan communities in back-reef depressions of Reunion Island (Mascarene Archipelago) through environmental DNA survey
inferred← citeshttps://doi.org/10.3390/d12040123openalex-snapshot
DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA
inferred← citeshttps://doi.org/10.5194/bg-17-5563-2020openalex-snapshot
Introduction: Process studies at the air–sea interface after atmospheric deposition in the Mediterranean Sea – objectives and strategy of the PEACETIME oceanographic campaign (May–June 2017)
inferred← citeshttps://doi.org/10.6084/m9.figshare.14374757openalex-snapshot
Additional file 1 of To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
inferred← citeshttps://doi.org/10.6084/m9.figshare.14374760openalex-snapshot
Additional file 2 of To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
inferred← citeshttps://doi.org/10.6084/m9.figshare.14374763openalex-snapshot
Additional file 3 of To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
inferred← citeshttps://doi.org/10.70675/0d2d4921z2c39z4b84zb3a5za8f479f89d14openalex-snapshot
Metabarcoding in the abyss : uncovering deep-sea biodiversity through environmental DNA
inferred← citeshttps://doi.org/10.70675/b1779c0czd493z4d41z807az5e71e566ac07openalex-snapshot
High-throughput sequencing techniques for the detection and survey of marine non-indigenous species : a valuable addition to traditional methods ?
inferred← citeshttps://doi.org/10.70675/cc55b037z6429z4986z8ed6z860fda6f0364openalex-snapshot
Résilience des écosystèmes hydrothermaux : résultats d’une expérience de perturbation au sein du champ hydrothermal Lucky Strike (dorsale médio-Atlantique)
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