To denoise or to cluster, that is not the question: optimizing pipelines for COI metabarcoding and metaphylogeography

Testing small‐scale ecological gradients and intraspecific differentiation for hundreds of kelp forest species using haplotypes from metabarcoding

(2021) Peter Shum et al.   MOLECULAR ECOLOGY

Validated removal of nuclear pseudogenes and sequencing artefacts from mitochondrial metabarcode data

(2021) Carmelo Andújar et al.   Molecular Ecology Resources

Environmental DNA surveys detect distinct metazoan communities across abyssal plains and seamounts in the western Clarion Clipperton Zone

(2020) Olivier Laroche et al.   MOLECULAR ECOLOGY

Comparing diversity levels in environmental samples: DNA sequence capture and metabarcoding approaches using 18S and COI genes

(2020) H Giebner et al.   Molecular Ecology Resources

Environmental DNA survey captures patterns of fish and invertebrate diversity across a tropical seascape

(2020) Bryan N. Nguyen et al.   Scientific Reports

A Systematic Review of Sources of Variability and Uncertainty in eDNA Data for Environmental Monitoring

(2020) Chloé Mathieu et al.   Frontiers in Ecology and Evolution

AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data

(2020) Xiyu Peng et al.   BIOINFORMATICS

Advances in metabarcoding techniques bring us closer to reliable monitoring of the marine benthos

(2020) Margaux Steyaert et al.   JOURNAL OF APPLIED ECOLOGY

Biases in bulk: DNA metabarcoding of marine communities and the methodology involved

(2020) Luna M. van der Loos et al.   MOLECULAR ECOLOGY

Reconstructing marine plankton food web interactions using DNA metabarcoding

(2020) Sara Zamora‐Terol et al.   MOLECULAR ECOLOGY

A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses

(2020) Devon R. O'Rourke et al.   Ecology and Evolution

Putting COI Metabarcoding in Context: The Utility of Exact Sequence Variants (ESVs) in Biodiversity Analysis

(2020) Teresita M. Porter et al.   Frontiers in Ecology and Evolution

Pan‐regional marine benthic cryptobiome biodiversity patterns revealed by metabarcoding Autonomous Reef Monitoring Structures

(2020) J.K. Pearman et al.   MOLECULAR ECOLOGY

Marine biomonitoring with eDNA: Can metabarcoding of water samples cut it as a tool for surveying benthic communities?

(2020) Adrià Antich et al.   MOLECULAR ECOLOGY

Metabarcoding From Microbes to Mammals: Comprehensive Bioassessment on a Global Scale

(2020) Zacchaeus G. Compson et al.   Frontiers in Ecology and Evolution

Metabarcoding free‐living marine nematodes using curated 18S and CO1 reference sequence databases for species‐level taxonomic assignments

(2019) Lara Macheriotou et al.   Ecology and Evolution

Improving eDNA‐based protist diversity assessments using networks of amplicon sequence variants

(2019) Dominik Forster et al.   ENVIRONMENTAL MICROBIOLOGY

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

DNA metabarcoding reveals modern and past eukaryotic communities in a high-mountain peat bog system

(2019) Sandra Garcés-Pastor et al.   JOURNAL OF PALEOLIMNOLOGY

Diatom DNA Metabarcoding for Biomonitoring: Strategies to Avoid Major Taxonomical and Bioinformatical Biases Limiting Molecular Indices Capacities

(2019) Kálmán Tapolczai et al.   Frontiers in Ecology and Evolution

From metabarcoding to metaphylogeography: separating the wheat from the chaff

(2019) Xavier Turon et al.   ECOLOGICAL APPLICATIONS

Biodiversity assessment of tropical shelf eukaryotic communities via pelagic eDNA metabarcoding

(2019) Judith Bakker et al.   Ecology and Evolution

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers

(2018) Owen S. Wangensteen et al.   PeerJ

Adapting metabarcoding-based benthic biomonitoring into routine marine ecological status assessment networks

(2018) Eva Aylagas et al.   ECOLOGICAL INDICATORS

Why the COI barcode should be the community DNA metabarcode for the metazoa

(2018) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

Metabarcoding of shrimp stomach content: Harnessing a natural sampler for fish biodiversity monitoring

(2018) Andjin Siegenthaler et al.   Molecular Ecology Resources

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Open-Source Sequence Clustering Methods Improve the State Of the Art

(2016) Evguenia Kopylova et al.   mSystems

Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life

(2016) Mikko Pentinsaari et al.   Scientific Reports

obitools: aunix-inspired software package for DNA metabarcoding

(2015) Frédéric Boyer et al.   Molecular Ecology Resources

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Clustering 16S rRNA for OTU prediction: a method of unsupervised Bayesian clustering

(2011) Xiaolin Hao et al.   BIOINFORMATICS

Phylogeny, phylogeography, phylobetadiversity and the molecular analysis of biological communities

(2011) B. C. Emerson et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Phylogeography: retrospect and prospect

(2008) John C. Avise   JOURNAL OF BIOGEOGRAPHY