Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

dbOTU3: A new implementation of distribution-based OTU calling

(2017) Scott W. Olesen et al.   PLoS One

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Coming of age: ten years of next-generation sequencing technologies

(2016) Sara Goodwin et al.   NATURE REVIEWS GENETICS

Large-Scale Monitoring of Plants through Environmental DNA Metabarcoding of Soil: Recovery, Resolution, and Annotation of Four DNA Markers

(2016) Nicole A. Fahner et al.   PLoS One

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Environmental DNA – An emerging tool in conservation for monitoring past and present biodiversity

(2015) Philip Francis Thomsen et al.   BIOLOGICAL CONSERVATION

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

(2015) Shawn P. Brown et al.   Fungal Ecology

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

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

Accurate multiplexing and filtering for high-throughput amplicon-sequencing

(2015) Philippe Esling et al.   NUCLEIC ACIDS RESEARCH

Fifteen forms of biodiversity trend in the Anthropocene

(2015) Brian J. McGill et al.   TRENDS IN ECOLOGY & EVOLUTION

Swarm v2: highly-scalable and high-resolution amplicon clustering

(2015) Frédéric Mahé et al.   PeerJ

A single genus in the gut microbiome reflects host preference and specificity

(2014) A Murat Eren et al.   ISME Journal

Correction: Symmetry: Modeling the Effects of Masking Noise, Axial Cueing and Salience

(2014) Chien-Chung Chen et al.   PLoS One

Waste Not, Want Not: Why Rarefying Microbiome Data Is Inadmissible

(2014) Paul J. McMurdie et al.   PLoS Computational Biology

Distribution-Based Clustering: Using Ecology To Refine the Operational Taxonomic Unit

(2013) Sarah P. Preheim et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

Towards next-generation biodiversity assessment using DNA metabarcoding

(2012) PIERRE TABERLET et al.   MOLECULAR ECOLOGY

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

(2011) Xiaolin Hao et al.   BIOINFORMATICS

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Reducing the Effects of PCR Amplification and Sequencing Artifacts on 16S rRNA-Based Studies

(2011) Patrick D. Schloss et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Ironing out the wrinkles in the rare biosphere through improved OTU clustering

(2010) Susan M. Huse et al.   ENVIRONMENTAL MICROBIOLOGY

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Insidious effects of sequencing errors on perceived diversity in molecular surveys

(2010) Ian A. Dickie   NEW PHYTOLOGIST

Introducing mothur: Open-Source, Platform-Independent, Community-Supported Software for Describing and Comparing Microbial Communities

(2009) P. D. Schloss et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Wrinkles in the rare biosphere: pyrosequencing errors can lead to artificial inflation of diversity estimates

(2009) Victor Kunin et al.   ENVIRONMENTAL MICROBIOLOGY

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

454 Pyrosequencing analyses of forest soils reveal an unexpectedly high fungal diversity

(2009) M. Buée et al.   NEW PHYTOLOGIST