A total crapshoot? Evaluating bioinformatic decisions in animal diet metabarcoding analyses

Identifying accurate metagenome and amplicon software via a meta-analysis of sequence to taxonomy benchmarking studies

(2019) Paul P. Gardner et al.   PeerJ

Metabarcoding a Diverse Arthropod Mock Community

(2019) Thomas W. A. Braukmann et al.   Molecular Ecology Resources

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

Counting with DNA in metabarcoding studies: How should we convert sequence reads to dietary data?

(2018) Bruce E. Deagle et al.   MOLECULAR ECOLOGY

How much is enough? Effects of technical and biological replication on metabarcoding dietary analysis

(2018) Vanessa A. Mata et al.   MOLECULAR ECOLOGY

Using DNA metabarcoding for simultaneous inference of common vampire bat diet and population structure

(2018) Kristine Bohmann et al.   Molecular Ecology Resources

Metabarcoding for the parallel identification of several hundred predators and their prey: Application to bat species diet analysis

(2018) Maxime Galan et al.   Molecular Ecology Resources

Disparities in second-generation DNA metabarcoding results exposed with accessible and repeatable workflows

(2018) Timothy J. Divoll et al.   Molecular Ecology Resources

Automated high throughput animal CO1 metabarcode classification

(2018) Teresita M. Porter et al.   Scientific Reports

Spatiotemporal and demographic variation in the diet of New Zealand lesser short-tailed bats (Mystacina tuberculata )

(2018) Zenon J. Czenze et al.   Ecology and Evolution

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve mycobiome data

(2018) Jonathan M. Palmer et al.   PeerJ

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

(2018) Alexandre Almeida et al.   GigaScience

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

Over 2.5 million COI sequences in GenBank and growing

(2018) Teresita M. Porter et al.   PLoS One

Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

(2018) Jacob T. Nearing et al.   PeerJ

Broadscale Ecological Patterns Are Robust to Use of Exact Sequence Variants versus Operational Taxonomic Units

(2018) Sydney I. Glassman et al.   mSphere

An improved method for utilizing high-throughput amplicon sequencing to determine the diets of insectivorous animals

(2018) Michelle A. Jusino et al.   Molecular Ecology Resources

Promises and pitfalls of using high-throughput sequencing for diet analysis

(2018) Antton Alberdi et al.   Molecular Ecology Resources

The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications

(2018) Rolf Henrik Nilsson et al.   NUCLEIC ACIDS RESEARCH

Table for five, please: Dietary partitioning in boreal bats

(2018) Eero J. Vesterinen et al.   Ecology and Evolution

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

(2017) Benjamin J Callahan et al.   ISME Journal

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Critical Assessment of Metagenome Interpretation—a benchmark of metagenomics software

(2017) Alexander Sczyrba et al.   NATURE METHODS

Pellets of proof: First glimpse of the dietary composition of adult odonates as revealed by metabarcoding of feces

(2017) Kari M. Kaunisto et al.   Ecology and Evolution

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

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

What you need is what you eat? Prey selection by the bat Myotis daubentonii

(2016) Eero J. Vesterinen et al.   MOLECULAR ECOLOGY

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

(2016) Nicholas A. Bokulich et al.   mSystems

Molecular evolution of a widely-adopted taxonomic marker (COI) across the animal tree of life

(2016) Mikko Pentinsaari et al.   Scientific Reports

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

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

Molecular detection of trophic interactions: emerging trends, distinct advantages, significant considerations and conservation applications

(2014) Elizabeth L. Clare   Evolutionary Applications

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample

(2010) J. G. Caporaso et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

DNA barcoding for ecologists

(2008) Alice Valentini et al.   TRENDS IN ECOLOGY & EVOLUTION