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

A validated workflow for rapid taxonomic assignment and monitoring of a national fauna of bees (Apiformes) using high throughput DNA barcoding

(2019) Thomas J. Creedy et al.   Molecular Ecology Resources

Heteroplasmy in the complete chicken mitochondrial genome

(2019) Yanqun Huang et al.   PLoS One

Validation of COI metabarcoding primers for terrestrial arthropods

(2019) Vasco Elbrecht et al.   PeerJ

A practical guide to DNA metabarcoding for entomological ecologists

(2019) Mingxin Liu et al.   ECOLOGICAL ENTOMOLOGY

Estimating intraspecific genetic diversity from community DNA metabarcoding data

(2018) Vasco Elbrecht et al.   PeerJ

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

(2018) Carmelo Andújar et al.   MOLECULAR ECOLOGY

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

(2017) Benjamin J Callahan et al.   ISME Journal

Metabarcoding of freshwater invertebrates to detect the effects of a pesticide spill

(2017) Carmelo Andújar et al.   MOLECULAR ECOLOGY

Repetitive transpositions of mitochondrial DNA sequences to the nucleus during the radiation of horseshoe bats (Rhinolophus, Chiroptera)

(2016) Huizhen Shi et al.   GENE

The effects of parameter choice on defining molecular operational taxonomic units and resulting ecological analyses of metabarcoding data

(2016) Elizabeth L. Clare et al.   GENOME

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

MEGAN Community Edition - Interactive Exploration and Analysis of Large-Scale Microbiome Sequencing Data

(2016) Daniel H. Huson et al.   PLoS Computational Biology

Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

(2015) Jullien M. Flynn et al.   Ecology and Evolution

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

A general species delimitation method with applications to phylogenetic placements

(2013) Jiajie Zhang et al.   BIOINFORMATICS

Reliable, verifiable and efficient monitoring of biodiversity via metabarcoding

(2013) Yinqiu Ji et al.   ECOLOGY LETTERS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

GenBank

(2013) Dennis A. Benson et al.   NUCLEIC ACIDS RESEARCH

PyroClean: Denoising Pyrosequences from Protein-Coding Amplicons for the Recovery of Interspecific and Intraspecific Genetic Variation

(2013) Ricardo Ramirez-Gonzalez et al.   PLoS One

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

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

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

Assessing and Improving Methods Used in Operational Taxonomic Unit-Based Approaches for 16S rRNA Gene Sequence Analysis

(2011) Patrick D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Mitochondrial DNA nucleoid structure

(2011) Daniel F. Bogenhagen   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Nuclear insertions of mitochondrial origin: Database updating and usefulness in cancer studies

(2011) Amanda Ramos et al.   MITOCHONDRION

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

Nuclear–Mitochondrial Sequences as Witnesses of Past Interbreeding and Population Diversity in the Jumping Bristletail Mesomachilis

(2010) Laura Baldo et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

Error-correcting barcoded primers for pyrosequencing hundreds of samples in multiplex

(2008) Micah Hamady et al.   NATURE METHODS

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