DNA metabarcoding of insects and allies: an evaluation of primers and pipelines

DNA barcoding implicates 23 species and four orders as potential pollinators of Chinese knotweed (Persicaria chinensis) in Peninsular Malaysia

(2015) M.-M. Wong et al.   BULLETIN OF ENTOMOLOGICAL RESEARCH

DNA barcoding and metabarcoding of standardized samples reveal patterns of marine benthic diversity

(2015) Matthieu Leray et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA barcodes for ecology, evolution, and conservation

(2015) W. John Kress et al.   TRENDS IN ECOLOGY & EVOLUTION

DNA metabarcoding and the cytochrome c oxidase subunit I marker: not a perfect match

(2014) B. E. Deagle et al.   Biology Letters

Using metabarcoding to ask if easily collected soil and leaf-litter samples can be used as a general biodiversity indicator

(2014) Chenxue Yang et al.   ECOLOGICAL INDICATORS

Second generation sequencing and morphological faecal analysis reveal unexpected foraging behaviour by Myotis nattereri (Chiroptera, Vespertilionidae) in winter

(2014) Paul R Hope et al.   Frontiers in Zoology

Environmental metabarcodes for insects:in silicoPCR reveals potential for taxonomic bias

(2014) Laurence J. Clarke et al.   Molecular Ecology Resources

Simultaneous assessment of the macrobiome and microbiome in a bulk sample of tropical arthropods through DNA metasystematics

(2014) J. Gibson et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From barcoding single individuals to metabarcoding biological communities: towards an integrative approach to the study of global biodiversity

(2014) Melania E. Cristescu   TRENDS IN ECOLOGY & EVOLUTION

Plant functional types and traits as biodiversity indicators for tropical forests: two biogeographically separated case studies including birds, mammals and termites

(2013) Andrew N. Gillison et al.   BIODIVERSITY AND CONSERVATION

PEAR: a fast and accurate Illumina Paired-End reAd mergeR

(2013) J. Zhang et al.   BIOINFORMATICS

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

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

(2013) Matthieu Leray et al.   Frontiers in Zoology

20 years since the introduction of DNA barcoding: from theory to application

(2013) Živa Fišer Pečnikar et al.   JOURNAL OF APPLIED GENETICS

Slowing PCR ramp speed reduces chimera formation from environmental samples

(2013) Julia L. Stevens et al.   JOURNAL OF MICROBIOLOGICAL METHODS

MEGA6: Molecular Evolutionary Genetics Analysis Version 6.0

(2013) Koichiro Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Who's for dinner? High-throughput sequencing reveals bat dietary differentiation in a biodiversity hotspot where prey taxonomy is largely undescribed

(2013) Joanna M. Burgar et al.   MOLECULAR ECOLOGY

A pragmatic approach to the analysis of diets of generalist predators: the use of next-generation sequencing with no blocking probes

(2013) J. Piñol et al.   Molecular Ecology Resources

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

SOAPBarcode: revealing arthropod biodiversity through assembly of Illumina shotgun sequences of PCR amplicons

(2013) Shanlin Liu et al.   Methods in Ecology and Evolution

Ultra-deep sequencing enables high-fidelity recovery of biodiversity for bulk arthropod samples without PCR amplification

(2013) Xin Zhou et al.   GigaScience

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers

(2012) Michael Quail et al.   BMC GENOMICS

Using dung beetles to evaluate the effects of urbanization on Atlantic Forest biodiversity

(2012) Vanesca Korasaki et al.   Insect Science

Bioinformatic challenges for DNA metabarcoding of plants and animals

(2012) ERIC COISSAC et al.   MOLECULAR ECOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Addressing challenges in the production and analysis of illumina sequencing data

(2011) Martin Kircher et al.   BMC GENOMICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

High-throughput sequencing offers insight into mechanisms of resource partitioning in cryptic bat species

(2011) Orly Razgour et al.   Ecology and Evolution

When species matches are unavailable are DNA barcodes correctly assigned to higher taxa? An assessment using sphingid moths

(2011) John Wilson et al.   BMC ECOLOGY

DNA Barcoding of Marine Metazoa

(2010) Ann Bucklin et al.   Annual Review of Marine Science

RDP3: a flexible and fast computer program for analyzing recombination

(2010) D. P. Martin et al.   BIOINFORMATICS

Mitochondrial heteroplasmy and DNA barcoding in Hawaiian Hylaeus (Nesoprosopis) bees (Hymenoptera: Colletidae)

(2010) Karl N Magnacca et al.   BMC EVOLUTIONARY BIOLOGY

Assessing the effects of primer specificity on eliminating numt coamplification in DNA barcoding: a case study from Orthoptera (Arthropoda: Insecta)

(2010) MATTHEW J. MOULTON et al.   Molecular Ecology Resources

Taxon-specific PCR for DNA barcoding arthropod prey in bat faeces

(2010) MATT R. K. ZEALE et al.   Molecular Ecology Resources

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

Phylogeny.fr: robust phylogenetic analysis for the non-specialist

(2008) A. Dereeper et al.   NUCLEIC ACIDS RESEARCH

Extreme diversity of tropical parasitoid wasps exposed by iterative integration of natural history, DNA barcoding, morphology, and collections

(2008) M. A. Smith et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Many species in one: DNA barcoding overestimates the number of species when nuclear mitochondrial pseudogenes are coamplified

(2008) H. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA BARCODING: CO1 DNA barcoding amphibians: take the chance, meet the challenge

(2007) M. ALEX SMITH et al.   Molecular Ecology Resources