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

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

(2017) Benjamin J Callahan et al.   ISME Journal

A new primer set for DNA metabarcoding of soil Metazoa

(2016) E. Capra et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

MEGA7: Molecular Evolutionary Genetics Analysis Version 7.0 for Bigger Datasets

(2016) Sudhir Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Improved taxonomic assignment of human intestinal 16S rRNA sequences by a dedicated reference database

(2015) Jarmo Ritari et al.   BMC GENOMICS

Meiofaunal community analysis by high-throughput sequencing: Comparison of extraction, quality filtering, and clustering methods

(2015) Pamela M. Brannock et al.   Marine Genomics

Metagenetic tools for the census of marine meiofaunal biodiversity: An overview

(2015) Laura Carugati et al.   Marine Genomics

Unveiling the Biodiversity of Deep-Sea Nematodes through Metabarcoding: Are We Ready to Bypass the Classical Taxonomy?

(2015) Antonio Dell’Anno et al.   PLoS One

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

Divergence thresholds and divergent biodiversity estimates: can metabarcoding reliably describe zooplankton communities?

(2015) Emily A. Brown et al.   Ecology and Evolution

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

De novo clustering methods outperform reference-based methods for assigning 16S rRNA gene sequences to operational taxonomic units

(2015) Sarah L. Westcott et al.   PeerJ

Metabarcoding Is Powerful yet Still Blind: A Comparative Analysis of Morphological and Molecular Surveys of Seagrass Communities

(2015) Dominique A. Cowart et al.   PLoS One

Linking operational clustered taxonomic units (OCTUs) from parallel ultra sequencing (PUS) to nematode species

(2015) D. L. Porazinska et al.   ZOOTAXA

Unraveling the outcome of 16S rDNA-based taxonomy analysis through mock data and simulations

(2014) Ali May et al.   BIOINFORMATICS

Limits to robustness and reproducibility in the demarcation of operational taxonomic units

(2014) Thomas S. B. Schmidt et al.   ENVIRONMENTAL MICROBIOLOGY

Systematics and DNA barcoding of free-living marine nematodes with emphasis on tropical desmodorids using nuclear SSU rDNA and mitochondrial COI sequences

(2014) Maickel Armenteros et al.   NEMATOLOGY

Meiofauna increases bacterial denitrification in marine sediments

(2014) S. Bonaglia et al.   Nature Communications

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

(2013) J. Zhang et al.   BIOINFORMATICS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

(2013) Wei Chen et al.   PLoS One

Adhoc: an R package to calculate ad hoc distance thresholds for DNA barcoding identification

(2013) Gontran Sonet et al.   ZooKeys

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

(2012) M. Kearse et al.   BIOINFORMATICS

The Magnitude of Global Marine Species Diversity

(2012) Ward Appeltans et al.   CURRENT BIOLOGY

Investigating the ecology and evolution of cryptic marine nematode species through quantitative real-time PCR of the ribosomal ITS region

(2012) S. DERYCKE et al.   Molecular Ecology Resources

Sequencing our way towards understanding global eukaryotic biodiversity

(2012) Holly M. Bik et al.   TRENDS IN ECOLOGY & 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

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

(2011) Xiaolin Hao et al.   BIOINFORMATICS

Impact of training sets on classification of high-throughput bacterial 16s rRNA gene surveys

(2011) Jeffrey J Werner et al.   ISME Journal

Metagenetic community analysis of microbial eukaryotes illuminates biogeographic patterns in deep-sea and shallow water sediments

(2011) HOLLY M. BIK et al.   MOLECULAR ECOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Depicting more accurate pictures of protistan community complexity using pyrosequencing of hypervariable SSU rRNA gene regions

(2010) Anke Behnke et al.   ENVIRONMENTAL MICROBIOLOGY

The contribution of deep-sea macrohabitat heterogeneity to global nematode diversity

(2010) Ann Vanreusel et al.   Marine Ecology-An Evolutionary Perspective

Ecometagenetics confirm high tropical rainforest nematode diversity

(2010) DOROTA L. PORAZINSKA et al.   MOLECULAR ECOLOGY

Exploring the Use of Cytochrome Oxidase c Subunit 1 (COI) for DNA Barcoding of Free-Living Marine Nematodes

(2010) Sofie Derycke et al.   PLoS One

Linking DNA sequences to morphology: cryptic diversity and population genetic structure in the marine nematodeThoracostoma trachygaster(Nematoda, Leptosomatidae)

(2010) Sofie Derycke et al.   ZOOLOGICA SCRIPTA

Disentangling taxonomy within the Rhabditis (Pellioditis) marina (Nematoda, Rhabditidae) species complex using molecular and morhological tools

(2010) S. DERYCKE et al.   ZOOLOGICAL JOURNAL OF THE LINNEAN SOCIETY

ESPRIT: estimating species richness using large collections of 16S rRNA pyrosequences

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

Description of Oncholaimus moanae sp. nov. (Nematoda: Oncholaimidae), with notes on feeding ecology based on isotopic and fatty acid composition

(2008) Daniel Leduc   JOURNAL OF THE MARINE BIOLOGICAL ASSOCIATION OF THE UNITED KINGDOM