Universal and blocking primer mismatches limit the use of high-throughput DNA sequencing for the quantitative metabarcoding of arthropods

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

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

Using Environmental DNA to Census Marine Fishes in a Large Mesocosm

(2014) Ryan P. Kelly et al.   PLoS One

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

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

(2013) Melissa E Carew et al.   Frontiers in Zoology

DNA metabarcoding multiplexing and validation of data accuracy for diet assessment: application to omnivorous diet

(2013) M. De Barba et al.   Molecular Ecology Resources

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

(2013) Bruce E. Deagle et al.   Molecular Ecology Resources

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

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

(2013) Elianne Egge et al.   PLoS One

Evaluating Detection Limits of Next-Generation Sequencing for the Surveillance and Monitoring of International Marine Pests

(2013) Xavier Pochon et al.   PLoS One

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

(2013) Xin Zhou et al.   GigaScience

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

Carnivore diet analysis based on next-generation sequencing: application to the leopard cat (Prionailurus bengalensis) in Pakistan

(2012) WASIM SHEHZAD et al.   MOLECULAR ECOLOGY

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

PCR Biases Distort Bacterial and Archaeal Community Structure in Pyrosequencing Datasets

(2012) Ameet J. Pinto et al.   PLoS One

Next Generation Sequencing to Define Prokaryotic and Fungal Diversity in the Bovine Rumen

(2012) Derrick E. Fouts et al.   PLoS One

Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

(2012) Douglas W. Yu et al.   Methods in Ecology and Evolution

Biodiversity assessment: State-of-the-art techniques in phylogenomics and species identification

(2011) P. R. Steele et al.   AMERICAN JOURNAL OF BOTANY

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Influence of management practices on large herbivore diet—Case of European bison in Białowieża Primeval Forest (Poland)

(2011) Rafał Kowalczyk et al.   FOREST ECOLOGY AND MANAGEMENT

Integrative analysis of environmental sequences using MEGAN4

(2011) D. H. Huson et al.   GENOME RESEARCH

Plant species richness belowground: higher richness and new patterns revealed by next-generation sequencing

(2011) INGA HIIESALU et al.   MOLECULAR ECOLOGY

Pyrosequencing of prey DNA in reptile faeces: analysis of earthworm consumption by slow worms

(2011) DAVID S. BROWN et al.   Molecular Ecology Resources

Molecular Diet Analysis of Two African Free-Tailed Bats (Molossidae) Using High Throughput Sequencing

(2011) Kristine Bohmann et al.   PLoS One

Soil fungal community structure along a soil health gradient in pea fields examined using deep amplicon sequencing

(2011) Lihui Xu et al.   SOIL BIOLOGY & BIOCHEMISTRY

TagCleaner: Identification and removal of tag sequences from genomic and metagenomic datasets

(2010) Robert Schmieder et al.   BMC BIOINFORMATICS

Pyrosequencing faecal DNA to determine diet of little penguins: is what goes in what comes out?

(2010) Bruce E. Deagle et al.   CONSERVATION GENETICS

New insights on diet variability revealed by DNA barcoding and high-throughput pyrosequencing: chamois diet in autumn as a case study

(2010) Gilles Rayé et al.   ECOLOGICAL RESEARCH

Quantifying microbial communities with 454 pyrosequencing: does read abundance count?

(2010) ANTHONY S. AMEND et al.   MOLECULAR ECOLOGY

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

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

Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures

(2009) Eeva M Soininen et al.   Frontiers in Zoology

Analysis of Australian fur seal diet by pyrosequencing prey DNA in faeces

(2009) BRUCE E. DEAGLE et al.   MOLECULAR ECOLOGY

Reproducibility of read numbers in high-throughput sequencing analysis of nematode community composition and structure

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

Evaluating high-throughput sequencing as a method for metagenomic analysis of nematode diversity

(2009) DOROTA L. PORAZINSKA et al.   Molecular Ecology Resources

New perspectives in diet analysis based on DNA barcoding and parallel pyrosequencing: thetrnL approach

(2009) ALICE VALENTINI et al.   Molecular Ecology Resources

A universal DNA mini-barcode for biodiversity analysis

(2008) Isabelle Meusnier et al.   BMC GENOMICS

Blocking primers to enhance PCR amplification of rare sequences in mixed samples – a case study on prey DNA in Antarctic krill stomachs

(2008) Hege Vestheim et al.   Frontiers in Zoology