Reference health
To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography
55/55 checkable references clean · checked 2026-07-14
Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a publisher retraction, withdrawal, or removal notice.
6 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.
The 55 checked references that resolve
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Environmental <scp>DNA</scp> metabarcoding: Transforming how we survey animal and plant communities
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Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks
resolves10.1016/bs.aecr.2020.01.011
Informing marine spatial planning decisions with environmental DNA
resolves10.3389/fevo.2020.581835
Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale
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A Systematic Review of Sources of Variability and Uncertainty in eDNA Data for Environmental Monitoring
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Trade-offs between reducing complex terminology and producing accurate interpretations from environmental DNA
resolves10.3389/fevo.2020.00248
Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis
resolves10.1002/ece3.4814
Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments
resolves10.1111/1462-2920.14764
Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants
resolves10.1002/ece3.6594
A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses
resolves10.1111/1755-0998.13201
Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes
resolves10.1002/eap.2036
From metabarcoding to metaphylogeography: separating the wheat from the chaff
resolves10.1038/ismej.2017.119
Exact sequence variants should replace operational taxonomic units in marker-gene data analysis
resolves10.1111/mec.14844
Why the COI barcode should be the community <scp>DNA</scp> metabarcode for the metazoa
resolves10.1111/MEC.15592
Biases in bulk: DNA metabarcoding of marine communities and the methodology involved
resolves10.3389/fevo.2019.00409
Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities
resolves10.1101/2020.06.24.169110
Consistent marine biogeographic boundaries across the tree of life despite centuries of human impacts
resolves10.1111/1365-2664.13729
Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos
resolves10.1111/mec.15555
Reconstructing marine plankton food web interactions using DNA metabarcoding
resolves10.1111/mec.15692
Pan‐regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures
resolves10.1101/717355
A flexible pipeline combining clustering and correction tools for prokaryotic and eukaryotic metabarcoding
resolves10.1038/s41598-020-63565-9
Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape
resolves10.1111/mec.15484
Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone
resolves10.1098/rstb.2011.0057
Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities
resolves10.1093/bioinformatics/btaa648
AmpliCI: a high-resolution model-based approach for denoising Illumina amplicon data
resolves10.1128/mSystems.00003-15
Open-Source Sequence Clustering Methods Improve the State Of the Art
resolves10.1101/081257
UNOISE2: improved error-correction for Illumina 16S and ITS amplicon sequencing
resolves10.1093/bioinformatics/btq725
Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering
resolves10.1111/1755-0998.12428
<scp>obitools</scp>: a <scp>unix</scp>‐inspired software package for <scp>DNA</scp> metabarcoding
resolves10.1038/s41587-019-0209-9
Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2
resolves10.7717/peerj.4644
Estimating intraspecific genetic diversity from community DNA metabarcoding data
resolves10.1111/mec.15851
Testing small‐scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding
resolves10.1002/edn3.44
Evaluating intraspecific genetic diversity using environmental DNA and denoising approach: A case study using tank water
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Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring
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DNA metabarcoding reveals modern and past eukaryotic communities in a high-mountain peat bog system
resolves10.1002/ece3.5871
Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding
resolves10.3390/d12040123
DNA Metabarcoding of Deep-Sea Sediment Communities Using COI: Community Assessment, Spatio-Temporal Patterns and Comparison with 18S rDNA
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Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?
resolves10.1111/1755-0998.13337
Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data
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DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers
resolves10.1038/srep35275
Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life
resolves10.1101/2021.01.08.425760
To denoise or to cluster? That is not the question. Optimizing pipelines for COI metabarcoding and metaphylogeography
resolves10.1111/j.2517-6161.1995.tb02031.x
Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing
resolves10.7717/peerj.5364
Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches
resolves10.22541/au.160071155.58915559
The influence of intraspecific sequence variation during DNA metabarcoding: A case study of eleven fungal species
resolves10.1101/2021.01.24.427982
Profile hidden Markov model sequence analysis can help remove putative pseudogenes from DNA barcoding and metabarcoding datasets
resolves10.1128/mSystems.00191-16
Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns
The 6 references without a DOI — listed, not checked
no DOI — not checkedZizka VMA, Weiss M, Leese F. Can metabarcoding resolve intraspecific genetic diversity changes to environmental stressors? A test case using river macrozoobenthos. Metabarcoding Metagenom. 2020;4:23–34.
no DOI — not checkedAntich A. DnoisE, Distance denoise by Entropy. GitHub repository. https://github.com/adriantich/DnoisE. Accessed 20 November 2020.
no DOI — not checkedHausser J, Strimmer K. Entropy inference and the James-Stein estimator, with application to nonlinear gene association networks. J Mach Learn Res. 2009;10:1469–84.
no DOI — not checkedWangensteen OS. Reference-databases Metabarpark. GitHub repository. http://github.com/metabarpark/Reference-databases. Accessed 23 December 2020.
no DOI — not checkedPagès H, Aboyoun P, Gentleman R, DebRoy S. Biostrings: Efficient manipulation of biological strings. R package version 2.58.0. https://bioconductor.org/packages/Biostrings. Accessed 10 March 2021.
no DOI — not checkedRatnasingham S, Hebert PDN. A DNA-based registry for all animal species: the Barcode Index Number (BIN) system. PLoS ONE. 2013;8(8):6.
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