Estimating intraspecific genetic diversity from community DNA metabarcoding data

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

Identifying North American freshwater invertebrates using DNA barcodes: are existing COI sequence libraries fit for purpose?

(2018) Colin J. Curry et al.   Freshwater Science

Metabarcoding Analyses Enable Differentiation of Both Interspecific Assemblages and Intraspecific Divergence in Habitats With Differing Management Practices

(2017) Pedro M Pedro et al.   ENVIRONMENTAL ENTOMOLOGY

Ecological dynamics and co-occurrence among marine phytoplankton, bacteria and myoviruses shows microdiversity matters

(2017) David M Needham et al.   ISME Journal

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

(2017) Benjamin J Callahan et al.   ISME Journal

A DNA barcode database of Australia’s freshwater macroinvertebrate fauna

(2017) M. E. Carew et al.   MARINE AND FRESHWATER RESEARCH

A from-benchtop-to-desktop workflow for validating HTS data and for taxonomic identification in diet metabarcoding studies

(2017) Emmanuel Corse et al.   Molecular Ecology Resources

Sorting things out: Assessing effects of unequal specimen biomass on DNA metabarcoding

(2017) Vasco Elbrecht et al.   Ecology and Evolution

Random sampling causes the low reproducibility of rare eukaryotic OTUs in Illumina COI metabarcoding

(2017) Matthieu Leray et al.   PeerJ

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

(2016) Melanie Schirmer et al.   BMC BIOINFORMATICS

Widely distributed and regionally isolated! Drivers of genetic structure in Gammarus fossarum in a human-impacted landscape

(2016) Martina Weiss et al.   BMC EVOLUTIONARY BIOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

The ecologist's field guide to sequence-based identification of biodiversity

(2016) Simon Creer et al.   Methods in Ecology and Evolution

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Population characteristics of a large whale shark aggregation inferred from seawater environmental DNA

(2016) Eva Egelyng Sigsgaard et al.   Nature Ecology & Evolution

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

Revisiting the phylogeography ofAsellus aquaticusin Europe: insights into cryptic diversity and spatiotemporal diversification

(2015) Lidia Sworobowicz et al.   FRESHWATER BIOLOGY

Tag jumps illuminated - reducing sequence-to-sample misidentifications in metabarcoding studies

(2015) Ida Baerholm Schnell et al.   Molecular Ecology Resources

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Primer and platform effects on 16S rRNA tag sequencing

(2015) Julien Tremblay et al.   Frontiers in Microbiology

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

(2015) Vasco Elbrecht et al.   PLoS One

Large-Scale Biomonitoring of Remote and Threatened Ecosystems via High-Throughput Sequencing

(2015) Joel F. Gibson et al.   PLoS One

AmpliconDuo: A Split-Sample Filtering Protocol for High-Throughput Amplicon Sequencing of Microbial Communities

(2015) Anja Lange et al.   PLoS One

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Minimum entropy decomposition: Unsupervised oligotyping for sensitive partitioning of high-throughput marker gene sequences

(2014) A Murat Eren et al.   ISME Journal

Next-generation DNA barcoding: using next-generation sequencing to enhance and accelerate DNA barcode capture from single specimens

(2014) Shadi Shokralla et al.   Molecular Ecology Resources

Genetic diversity and dispersal potential of the stonefly Dinocras cephalotes in a central European low mountain range

(2014) Vasco Elbrecht et al.   Freshwater Science

Identification of 100 fundamental ecological questions

(2013) William J. Sutherland et al.   JOURNAL OF ECOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Genetic diversity in widespread species is not congruent with species richness in alpine plant communities

(2012) Pierre Taberlet et al.   ECOLOGY LETTERS

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

Cryptic biodiversity loss linked to global climate change

(2011) M. Bálint et al.   Nature Climate Change

Genetic and morphological approaches to the problematic presence of threeHydropsychespecies of thepellucidulagroup (Trichoptera: Hydropsychidae) in the westernmost Mediterranean Basin

(2010) Cesc Múrria et al.   AQUATIC INSECTS

Genes in Streams: Using DNA to Understand the Movement of Freshwater Fauna and Their Riverine Habitat

(2009) Jane M. Hughes et al.   BIOSCIENCE