MAUI‐seq: Metabarcoding using amplicons with unique molecular identifiers to improve error correction

Ultrasensitive DNA Immune Repertoire Sequencing Using Unique Molecular Identifiers

(2020) Gustav Johansson et al.   CLINICAL CHEMISTRY

Host‐specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae

(2019) Stéphane Boivin et al.   NEW PHYTOLOGIST

Scaling up DNA barcoding - Primer sets for simple and cost efficient arthropod systematics by multiplex PCR and Illumina amplicon sequencing

(2018) Henrik Krehenwinkel et al.   Methods in Ecology and Evolution

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

(2018) Jonathan M. Palmer et al.   PeerJ

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

(2018) Nicholas A. Bokulich et al.   Microbiome

“Pitfalls in relative abundance estimation using eDNA metabarcoding”

(2018) Vera G. Fonseca   Molecular Ecology Resources

Deciphering intra-species bacterial diversity of meat and seafood spoilage microbiota using gyrB amplicon sequencing: A comparative analysis with 16S rDNA V3-V4 amplicon sequencing

(2018) Simon Poirier et al.   PLoS One

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

(2018) Jacob T. Nearing et al.   PeerJ

Environmental DNA metabarcoding: Transforming how we survey animal and plant communities

(2017) Kristy Deiner et al.   MOLECULAR ECOLOGY

The empirical Bayes estimators of fine-scale population structure in high gene flow species

(2017) Shuichi Kitada et al.   Molecular Ecology Resources

Large-scale differences in microbial biodiversity discovery between 16S amplicon and shotgun sequencing

(2017) Michael Tessler et al.   Scientific Reports

Generic Amplicon Deep Sequencing to Determine Ilarvirus Species Diversity in Australian Prunus

(2017) Wycliff M. Kinoti et al.   Frontiers in Microbiology

Application of Stochastic Labeling with Random-Sequence Barcodes for Simultaneous Quantification and Sequencing of Environmental 16S rRNA Genes

(2017) Tatsuhiko Hoshino et al.   PLoS One

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

Bacterial populations in juvenile maize rhizospheres originate from both seed and soil

(2016) David Johnston-Monje et al.   PLANT AND SOIL

A method for high precision sequencing of near full-length 16S rRNA genes on an Illumina MiSeq

(2016) Catherine M. Burke et al.   PeerJ

Benefits and Challenges with Applying Unique Molecular Identifiers in Next Generation Sequencing to Detect Low Frequency Mutations

(2016) Ruqin Kou et al.   PLoS One

Polymerase matters: non-proofreading enzymes inflate fungal community richness estimates by up to 15 %

(2015) Alena K. Oliver et al.   Fungal Ecology

Quantitative Profiling of Immune Repertoires for Minor Lymphocyte Counts Using Unique Molecular Identifiers

(2015) Evgeny S. Egorov et al.   JOURNAL OF IMMUNOLOGY

Estimating Bacterial Diversity for Ecological Studies: Methods, Metrics, and Assumptions

(2015) Julia Birtel et al.   PLoS One

Can DNA-Based Ecosystem Assessments Quantify Species Abundance? Testing Primer Bias and Biomass—Sequence Relationships with an Innovative Metabarcoding Protocol

(2015) Vasco Elbrecht et al.   PLoS One

Towards error-free profiling of immune repertoires

(2014) Mikhail Shugay et al.   NATURE METHODS

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

(2013) J. Zhang et al.   BIOINFORMATICS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

Practical innovations for high-throughput amplicon sequencing

(2013) Derek S Lundberg et al.   NATURE METHODS

Fungal community analysis by high-throughput sequencing of amplified markers - a user's guide

(2013) Björn D. Lindahl et al.   NEW PHYTOLOGIST

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

High-Throughput Sequencing: A Roadmap Toward Community Ecology

(2013) Timothée Poisot et al.   Ecology and Evolution

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Accurate sampling and deep sequencing of the HIV-1 protease gene using a Primer ID

(2011) C. B. Jabara et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

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