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Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction
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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/ece3.2220openalex-snapshot
Leaf litter arthropod responses to tropical forest restoration
inferredcites →https://doi.org/10.1002/ece3.3192openalex-snapshot
Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding
inferredcites →https://doi.org/10.1002/ece3.4013openalex-snapshot
Needle in a haystack? A comparison of eDNA metabarcoding and targeted qPCR for detection of the great crested newt ( Triturus cristatus )
inferredcites →https://doi.org/10.1002/ece3.4839openalex-snapshot
Toward accurate species‐level metabarcoding of arthropod communities from the tropical forest canopy
inferredcites →https://doi.org/10.1007/978-1-61779-870-2_2openalex-snapshot
OligoTag: A Program for Designing Sets of Tags for Next-Generation Sequencing of Multiplexed Samples
inferredcites →https://doi.org/10.1016/j.ecolind.2019.01.023openalex-snapshot
The devil is in the detail: Metabarcoding of arthropods provides a sensitive measure of biodiversity response to forest stand composition compared with surrogate measures of biodiversity
inferredcites →https://doi.org/10.1016/j.soilbio.2016.02.003openalex-snapshot
A method for simultaneous measurement of soil bacterial abundances and community composition via 16S rRNA gene sequencing
inferredcites →https://doi.org/10.1016/j.tree.2014.04.003openalex-snapshot
Environmental DNA for wildlife biology and biodiversity monitoring
inferredcites →https://doi.org/10.1016/j.watres.2018.03.003openalex-snapshot
Implementation options for DNA-based identification into ecological status assessment under the European Water Framework Directive
inferredcites →https://doi.org/10.1016/s0169-5347(01)02151-6openalex-snapshot
Mitochondrial pseudogenes: evolution's misplaced witnesses
inferredcites →https://doi.org/10.1038/ncomms1095openalex-snapshot
Second-generation environmental sequencing unmasks marine metazoan biodiversity
inferredcites →https://doi.org/10.1038/nmeth.3869openalex-snapshot
DADA2: High-resolution sample inference from Illumina amplicon data
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/srep16498openalex-snapshot
Intrinsic challenges in ancient microbiome reconstruction using 16S rRNA gene amplification
inferredcites →https://doi.org/10.1073/pnas.1424997112openalex-snapshot
DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity
inferredcites →https://doi.org/10.1093/bioinformatics/bty454openalex-snapshot
MIDORI server: a webserver for taxonomic assignment of unknown metazoan mitochondrial-encoded sequences using a curated database
inferredcites →https://doi.org/10.1093/bioinformatics/bty560openalex-snapshot
fastp: an ultra-fast all-in-one FASTQ preprocessor
inferredcites →https://doi.org/10.1093/gigascience/giz029openalex-snapshot
An efficient and robust laboratory workflow and tetrapod database for larger scale environmental DNA studies
inferredcites →https://doi.org/10.1093/gigascience/giz092openalex-snapshot
Prospects and challenges of implementing DNA metabarcoding for high-throughput insect surveillance
inferredcites →https://doi.org/10.1093/nar/gkv107openalex-snapshot
Accurate multiplexing and filtering for high-throughput amplicon-sequencing
inferredcites →https://doi.org/10.1098/rsbl.2014.0562openalex-snapshot
DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match
inferredcites →https://doi.org/10.1101/081257openalex-snapshot
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
inferredcites →https://doi.org/10.1111/1365-2664.13411openalex-snapshot
Shifting up a gear with iDNA : From mammal detection events to standardised surveys
inferredcites →https://doi.org/10.1111/1755-0998.12180openalex-snapshot
Detecting an elusive invasive species: a diagnostic PCR to detect B urmese python in F lorida waters and an assessment of persistence of environmental DNA
inferredcites →https://doi.org/10.1111/1755-0998.12188openalex-snapshot
DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet
inferredcites →https://doi.org/10.1111/1755-0998.12265openalex-snapshot
Environmental metabarcodes for insects: in silico PCR reveals potential for taxonomic bias
inferredcites →https://doi.org/10.1111/1755-0998.12355openalex-snapshot
Universal and blocking primer mismatches limit the use of high‐throughput DNA sequencing for the quantitative metabarcoding of arthropods
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/10.1111/1755-0998.12740openalex-snapshot
Genetic monitoring of open ocean biodiversity: An evaluation of DNA metabarcoding for processing continuous plankton recorder samples
inferredcites →https://doi.org/10.1111/1755-0998.12891openalex-snapshot
Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure
inferredcites →https://doi.org/10.1111/1755-0998.12895openalex-snapshot
Minimizing polymerase biases in metabarcoding
inferredcites →https://doi.org/10.1111/1755-0998.13018openalex-snapshot
Assessing the influence of sample tagging and library preparation on DNA metabarcoding
inferredcites →https://doi.org/10.1111/1755-0998.13057openalex-snapshot
SPIKEPIPE: A metagenomic pipeline for the accurate quantification of eukaryotic species occurrences and intraspecific abundance change using DNA barcodes or mitogenomes
inferredcites →https://doi.org/10.1111/1755-0998.13061openalex-snapshot
Genome‐skimming provides accurate quantification for pollen mixtures
inferredcites →https://doi.org/10.1111/1755-0998.13294openalex-snapshot
MAUI‐seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction
inferredcites →https://doi.org/10.1111/2041-210x.12849openalex-snapshot
Scrutinizing key steps for reliable metabarcoding of environmental samples
inferredcites →https://doi.org/10.1111/2041-210x.13265openalex-snapshot
Semi‐quantitative characterisation of mixed pollen samples using MinION sequencing and Reverse Metagenomics (RevMet)
inferredcites →https://doi.org/10.1111/biom.13503openalex-snapshot
A multiview model for relative and absolute microbial abundances
inferredcites →https://doi.org/10.1111/ddi.12972openalex-snapshot
The biodiversity benefit of native forests and mixed‐species plantations over monoculture plantations
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.2009.04158.xopenalex-snapshot
Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05418.xopenalex-snapshot
Monitoring endangered freshwater biodiversity using environmental DNA
inferredcites →https://doi.org/10.1111/j.1365-294x.2011.05424.xopenalex-snapshot
Carnivore diet analysis based on next‐generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05470.xopenalex-snapshot
Towards next‐generation biodiversity assessment using DNA metabarcoding
inferredcites →https://doi.org/10.1111/j.1365-294x.2012.05505.xopenalex-snapshot
The future of environmental DNA in ecology
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/mec.13761openalex-snapshot
High‐throughput metabarcoding of eukaryotic diversity for environmental monitoring of offshore oil‐drilling activities
inferredcites →https://doi.org/10.1111/mec.13770openalex-snapshot
Plant diversity accurately predicts insect diversity in two tropical landscapes
inferredcites →https://doi.org/10.1111/mec.14350openalex-snapshot
Environmental DNA metabarcoding: Transforming how we survey animal and plant communities
inferredcites →https://doi.org/10.1111/mec.14734openalex-snapshot
Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?
inferredcites →https://doi.org/10.1111/mec.14776openalex-snapshot
The choice of universal primers and the characteristics of the species mixture determine when DNA metabarcoding can be quantitative
inferredcites →https://doi.org/10.1111/mec.15472openalex-snapshot
Ecosystems monitoring powered by environmental genomics: A review of current strategies with an implementation roadmap
inferredcites →https://doi.org/10.1111/rec.12868openalex-snapshot
DNA metabarcoding—a new approach to fauna monitoring in mine site restoration
inferredcites →https://doi.org/10.1128/aem.05220-11openalex-snapshot
Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification
inferredcites →https://doi.org/10.1128/aem.64.10.3724-3730.1998openalex-snapshot
Bias in Template-to-Product Ratios in Multitemplate PCR
inferredcites →https://doi.org/10.1186/1471-2105-11-206openalex-snapshot
Comparative performances of DNA barcoding across insect orders
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/10.1186/2049-2618-2-6openalex-snapshot
An improved dual-indexing approach for multiplexed 16S rRNA gene sequencing on the Illumina MiSeq platform
inferredcites →https://doi.org/10.1186/s13104-016-2064-9openalex-snapshot
DAMe: a toolkit for the initial processing of datasets with PCR replicates of double-tagged amplicons for DNA metabarcoding analyses
inferredcites →https://doi.org/10.1186/s40168-018-0491-7openalex-snapshot
Absolute quantitation of microbiota abundance in environmental samples
inferredcites →https://doi.org/10.1371/journal.pcbi.1005404openalex-snapshot
Metacoder: An R package for visualization and manipulation of community taxonomic diversity data
inferredcites →https://doi.org/10.1371/journal.pone.0013042openalex-snapshot
An Efficient Multistrategy DNA Decontamination Procedure of PCR Reagents for Hypersensitive PCR Applications
inferredcites →https://doi.org/10.1371/journal.pone.0017497openalex-snapshot
Environmental Barcoding: A Next-Generation Sequencing Approach for Biomonitoring Applications Using River Benthos
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.0124671openalex-snapshot
From Benchtop to Desktop: Important Considerations when Designing Amplicon Sequencing Workflows
inferredcites →https://doi.org/10.1371/journal.pone.0148698openalex-snapshot
Indexed PCR Primers Induce Template-Specific Bias in Large-Scale DNA Sequencing Studies
inferredcites →https://doi.org/10.1371/journal.pone.0169431openalex-snapshot
Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes
inferredcites →https://doi.org/10.18637/jss.v067.i01openalex-snapshot
Fitting Linear Mixed-Effects Models Using lme4
inferredcites →https://doi.org/10.32614/r.manualsopenalex-snapshot
R: A Language and Environment for Statistical Computing
inferredcites →https://doi.org/10.3354/meps12165openalex-snapshot
Assessing the trophic ecology of top predators across a recolonisation frontier using DNA metabarcoding of diets
inferredcites →https://doi.org/10.3389/fevo.2019.00434openalex-snapshot
Studying Ecosystems With DNA Metabarcoding: Lessons From Biomonitoring of Aquatic Macroinvertebrates
inferredcites →https://doi.org/10.5061/dryad.ncjsxksrcopenalex-snapshot
Biodiversity Soup II: A bulk‐sample metabarcoding pipeline emphasizing error reduction
inferredcites →https://doi.org/10.7554/elife.46923openalex-snapshot
Consistent and correctable bias in metagenomic sequencing experiments
inferredcites →https://doi.org/10.7717/peerj.2584openalex-snapshot
VSEARCH: a versatile open source tool for metagenomics
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.9.161359zenodo-depositor-declared
A DNA metabarcoding workflow for the detection of terrestrial gastropods from ingested DNA
inferred← citeshttps://doi.org/10.1002/ece3.11486openalex-snapshot
Diet components associated with specific bacterial taxa shape overall gut community compositions in omnivorous African viverrids
inferred← citeshttps://doi.org/10.1002/ece3.11631openalex-snapshot
Experimental evaluation of genetic variability based on DNA metabarcoding from the aquatic environment: Insights from the Leray COI fragment
inferred← citeshttps://doi.org/10.1002/ece3.72954openalex-snapshot
Characterization of the Omnivorous Lygus lineolaris Diet in a Strawberry Field by Metataxonomy
inferred← citeshttps://doi.org/10.1002/ece3.8239openalex-snapshot
Revisiting the effect of PCR replication and sequencing depth on biodiversity metrics in environmental DNA metabarcoding
inferred← citeshttps://doi.org/10.1002/edn3.467openalex-snapshot
Detection of fish sedimentary DNA in aquatic systems: A review of methodological challenges and future opportunities
inferred← citeshttps://doi.org/10.1002/edn3.542openalex-snapshot
Identifying archived insect bulk samples using DNA metabarcoding: A case study using the long‐term Rothamsted Insect Survey
inferred← citeshttps://doi.org/10.1002/edn3.70168openalex-snapshot
Comparative Efficiency of Multiple eDNA Sampling Methods for Monitoring Vertebrate Diversity in Mountainous Region
inferred← citeshttps://doi.org/10.1002/ps.70345openalex-snapshot
DNA metabarcoding‐based monitoring of insect biodiversity across agricultural ecosystems in China
inferred← citeshttps://doi.org/10.1007/s00227-025-04609-4openalex-snapshot
An innovative approach for marine macro-organism monitoring: methodology and future perspectives of environmental DNA (eDNA) technology
inferred← citeshttps://doi.org/10.1016/j.cub.2021.12.014openalex-snapshot
Airborne environmental DNA for terrestrial vertebrate community monitoring
inferred← citeshttps://doi.org/10.1016/j.cub.2022.12.049openalex-snapshot
Food webs reveal coexistence mechanisms and community organization in carnivores
inferred← citeshttps://doi.org/10.1016/j.cub.2025.11.017openalex-snapshot
Invasive predator reshapes island trophic network and biogeography
inferred← citeshttps://doi.org/10.1016/j.ejsobi.2026.103879openalex-snapshot
Large soil samples for large soil organisms – modification of eDNA extraction method for investigation of soil invertebrate communities
inferred← citeshttps://doi.org/10.1016/j.foodcont.2025.111338openalex-snapshot
Beyond mislabelling: Chinese fish balls authentication by metabarcoding allows unveiling hidden mammal and avian species
inferred← citeshttps://doi.org/10.1016/j.jfca.2023.105559openalex-snapshot
Metabarcoding for the authentication of complex seafood products: The fish burger case
inferred← citeshttps://doi.org/10.1016/j.pedobi.2025.151022openalex-snapshot
Metabarcoding of a mock community of soil invertebrates: DNA extraction, false positives, and data filtration
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2024.173621openalex-snapshot
Effectiveness of eDNA for monitoring riverine macroinvertebrates
inferred← citeshttps://doi.org/10.1016/j.scitotenv.2024.176892openalex-snapshot
Cascading impacts of nitrogen deposition on soil microbiome and herbivore communities in desert steppes
inferred← citeshttps://doi.org/10.1016/j.soilbio.2026.110177openalex-snapshot
Gut-content metabarcoding reveals opportunistic earthworm predation by the invasive terrestrial flatworm Obama nungara
inferred← citeshttps://doi.org/10.1038/s42003-026-09950-yopenalex-snapshot
Advancing airborne eDNA sampling methods for monitoring diverse terrestrial vertebrate communities
inferred← citeshttps://doi.org/10.1080/01621459.2024.2412362openalex-snapshot
eDNAPlus: A Unifying Modeling Framework for DNA-based Biodiversity Monitoring
inferred← citeshttps://doi.org/10.1093/biosci/biaf140openalex-snapshot
Unlocking natural history collections to improve eDNA reference databases and biodiversity monitoring
inferred← citeshttps://doi.org/10.1093/gigascience/giac065openalex-snapshot
Toward global integration of biodiversity big data: a harmonized metabarcode data generation module for terrestrial arthropods
inferred← citeshttps://doi.org/10.1093/jee/toag264openalex-snapshot
Quantitative metabarcoding for invertebrate pest monitoring and management
inferred← citeshttps://doi.org/10.1098/rstb.2023.0123openalex-snapshot
Combining environmental DNA and remote sensing for efficient, fine-scale mapping of arthropod biodiversity
inferred← citeshttps://doi.org/10.1101/2023.10.03.560640openalex-snapshot
Towards quantitative DNA Metabarcoding: A method to overcome PCR amplification bias
inferred← citeshttps://doi.org/10.1101/2025.01.29.635447openalex-snapshot
Arctic plant species display contrasting levels of chloroplast DNA copy numbers
inferred← citeshttps://doi.org/10.1101/2025.05.23.655448openalex-snapshot
Metabarcoding reveals the effect of land cover and temporal variations on the diet of Brown long-eared and Soprano pipistrelle bats within a unique European habitat, the pasture dominated landscapes of Ireland
inferred← citeshttps://doi.org/10.1111/1744-7917.70074openalex-snapshot
Understanding biological control function and trophic interaction dynamics of an artificially released predatory bug by DNA metabarcoding
inferred← citeshttps://doi.org/10.1111/1755-0998.13502openalex-snapshot
Coming of age for COI metabarcoding of whole organism community DNA: Towards bioinformatic harmonisation
inferred← citeshttps://doi.org/10.1111/1755-0998.13512openalex-snapshot
Strategies for sample labelling and library preparation in DNA metabarcoding studies
inferred← citeshttps://doi.org/10.1111/1755-0998.13703openalex-snapshot
Extracting abundance information from DNA ‐based data
inferred← citeshttps://doi.org/10.1111/1755-0998.13794openalex-snapshot
Replicate DNA metabarcoding can discriminate seasonal and spatial abundance shifts in river macroinvertebrate assemblages
inferred← citeshttps://doi.org/10.1111/1755-0998.13840openalex-snapshot
Airborne environmental DNA captures terrestrial vertebrate diversity in nature
inferred← citeshttps://doi.org/10.1111/1755-0998.13855openalex-snapshot
Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA
inferred← citeshttps://doi.org/10.1111/1755-0998.14097openalex-snapshot
EntoSieve: Automated Size‐Sorting of Insect Bulk Samples to Aid Accurate Megabarcoding and Metabarcoding
inferred← citeshttps://doi.org/10.1111/1755-0998.70056openalex-snapshot
Airborne eDNA Reveals Resource‐Based Assembly of Frugivorous Vertebrates
inferred← citeshttps://doi.org/10.1111/1755-0998.70088openalex-snapshot
Moss‐Accumulated eDNA Is a Promising Source for Terrestrial Biodiversity Surveys Across the Tree of Life and Biomes
inferred← citeshttps://doi.org/10.1111/2041-210x.14073openalex-snapshot
Optimizing insect metabarcoding using replicated mock communities
inferred← citeshttps://doi.org/10.1111/csp2.70254openalex-snapshot
Carbon finance initiatives can provide biodiversity benefits
inferred← citeshttps://doi.org/10.1111/ecog.07461openalex-snapshot
Assembly processes inferred from eDNA surveys of a pond metacommunity are consistent with known species ecologies
inferred← citeshttps://doi.org/10.1111/mec.16747openalex-snapshot
Phylogenetic diversity only weakly mitigates climate‐change‐driven biodiversity loss in insect communities
inferred← citeshttps://doi.org/10.1111/rec.70432openalex-snapshot
Selective seasonal foraging behavior of herbivores on a Danish island demonstrated by DNA metabarcoding
inferred← citeshttps://doi.org/10.22541/au.166756789.99942137/v1openalex-snapshot
Experimental evaluation of species and genetic variability based on DNA metabarcoding from the aquatic environment: extra OTUs formed by NUMTS may reduce the diversity of ASVs
inferred← citeshttps://doi.org/10.31083/fbs26247openalex-snapshot
Evaluation of Fish Species Detection in the Northwestern Pacific using eDNA Metabarcoding: A Mock Community Approach
inferred← citeshttps://doi.org/10.3389/fevo.2021.783546openalex-snapshot
Snow Leopard Dietary Preferences and Livestock Predation Revealed by Fecal DNA Metabarcoding: No Evidence for Apparent Competition Between Wild and Domestic Prey
inferred← citeshttps://doi.org/10.3389/fevo.2022.822648openalex-snapshot
DNA Metabarcoding Enables High-Throughput Detection of Spotted Wing Drosophila (Drosophila suzukii) Within Unsorted Trap Catches
inferred← citeshttps://doi.org/10.3389/fevo.2024.1411388openalex-snapshot
Navigating diversity: primer impact on arthropod recovery in molecular environmental monitoring in tropical Amazon
inferred← citeshttps://doi.org/10.3389/fmicb.2022.969799openalex-snapshot
Does filter pore size introduce bias in DNA sequence-based plankton community studies?
inferred← citeshttps://doi.org/10.3390/d18020120openalex-snapshot
Environmental DNA Metabarcoding of a Seagrass Meadow in Vostok Bay (Peter the Great Bay, Sea of Japan): A COI Snapshot of Coastal Biodiversity and Its Limitations
inferred← citeshttps://doi.org/10.3390/jmse10030375openalex-snapshot
Evaluating eDNA for Use within Marine Environmental Impact Assessments
inferred← citeshttps://doi.org/10.3897/mbmg.7.86883openalex-snapshot
Pollen metabarcoding of museum specimens and recently collected bumblebees (Bombus) indicates foraging shifts
inferred← citeshttps://doi.org/10.5852/naturae2024a3openalex-snapshot
La reconnaissance des espèces basée sur l’ADN : applications, perspectives et défisen milieu continental terrestre
inferred← citeshttps://doi.org/10.7717/peerj.16253openalex-snapshot
taxalogue: a toolkit to create comprehensive CO1 reference databases
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