Accurate multiplexing and filtering for high-throughput amplicon-sequencing

SASI-Seq: sample assurance Spike-Ins, and highly differentiating 384 barcoding for Illumina sequencing

(2014) Michael A Quail et al.   BMC GENOMICS

Environmental monitoring through protist next-generation sequencing metabarcoding: assessing the impact of fish farming on benthic foraminifera communities

(2014) Jan Pawlowski et al.   Molecular Ecology Resources

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

Ancient DNA complements microfossil record in deep-sea subsurface sediments

(2013) F. Lejzerowicz et al.   Biology Letters

Environmental monitoring using next generation sequencing: rapid identification of macroinvertebrate bioindicator species

(2013) Melissa E Carew et al.   Frontiers in Zoology

A Unique Signal Distorts the Perception of Species Richness and Composition in High-Throughput Sequencing Surveys of Microbial Communities: a Case Study of Fungi in Indoor Dust

(2013) Rachel I. Adams et al.   MICROBIAL ECOLOGY

Illumina Sequencing of 16S rRNA Tag Revealed Spatial Variations of Bacterial Communities in a Mangrove Wetland

(2013) Xiao-Tao Jiang et al.   MICROBIAL ECOLOGY

Modular tagging of amplicons using a single PCR for high-throughput sequencing

(2013) Laurence J. Clarke et al.   Molecular Ecology Resources

Quantifying sequence proportions in a DNA-based diet study using Ion Torrent amplicon sequencing: which counts count?

(2013) Bruce E. Deagle et al.   Molecular Ecology Resources

The role of replicates for error mitigation in next-generation sequencing

(2013) Kimberly Robasky et al.   NATURE REVIEWS GENETICS

Deep Sequencing of Subseafloor Eukaryotic rRNA Reveals Active Fungi across Marine Subsurface Provinces

(2013) William Orsi et al.   PLoS One

Improved Inference of Taxonomic Richness from Environmental DNA

(2013) Matthew J. Morgan et al.   PLoS One

454 Pyrosequencing to Describe Microbial Eukaryotic Community Composition, Diversity and Relative Abundance: A Test for Marine Haptophytes

(2013) Elianne Egge et al.   PLoS One

PNAS Plus: From the Cover: Microbial biogeography of wine grapes is conditioned by cultivar, vintage, and climate

(2013) N. A. Bokulich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Illumina metabarcoding of a soil fungal community

(2013) Philipp-André Schmidt et al.   SOIL BIOLOGY & BIOCHEMISTRY

Illumina sequencing of the V4 hypervariable region 16S rRNA gene reveals extensive changes in bacterial communities in the cecum following carbohydrate oral infusion and development of early-stage acute laminitis in the horse

(2013) Michael M. Moreau et al.   VETERINARY MICROBIOLOGY

High sensitivity of 454 pyrosequencing for detection of rare species in aquatic communities

(2013) Aibin Zhan et al.   Methods in Ecology and Evolution

Cohabiting family members share microbiota with one another and with their dogs

(2013) Se Jin Song et al.   eLife

Don't make a mista(g)ke: is tag switching an overlooked source of error in amplicon pyrosequencing studies?

(2012) Tor Carlsen et al.   Fungal Ecology

Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms

(2012) J Gregory Caporaso et al.   ISME Journal

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Sample richness and genetic diversity as drivers of chimera formation in nSSU metagenetic analyses

(2012) V. G. Fonseca et al.   NUCLEIC ACIDS RESEARCH

The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy

(2012) Laure Guillou et al.   NUCLEIC ACIDS RESEARCH

Amplification by PCR Artificially Reduces the Proportion of the Rare Biosphere in Microbial Communities

(2012) Juan M. Gonzalez et al.   PLoS One

Groundtruthing Next-Gen Sequencing for Microbial Ecology–Biases and Errors in Community Structure Estimates from PCR Amplicon Pyrosequencing

(2012) Charles K. Lee et al.   PLoS One

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

Barcoded Primers Used in Multiplex Amplicon Pyrosequencing Bias Amplification

(2011) David Berry et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Generation of Multimillion-Sequence 16S rRNA Gene Libraries from Complex Microbial Communities by Assembling Paired-End Illumina Reads

(2011) Andrea K. Bartram et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Novel lineages of Southern Ocean deep-sea foraminifera revealed by environmental DNA sequencing

(2011) Jan Pawlowski et al.   DEEP-SEA RESEARCH PART II-TOPICAL STUDIES IN OCEANOGRAPHY

Reproducibility and quantitation of amplicon sequencing-based detection

(2011) Jizhong Zhou et al.   ISME Journal

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Comparison of Normalization Methods for Construction of Large, Multiplex Amplicon Pools for Next-Generation Sequencing

(2010) J. K. Harris et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A 454 multiplex sequencing method for rapid and reliable genotyping of highly polymorphic genes in large-scale studies

(2010) Maxime Galan et al.   BMC GENOMICS

Molecular evidence for widespread occurrence of Foraminifera in soils

(2010) Franck Lejzerowicz et al.   ENVIRONMENTAL MICROBIOLOGY

Experimental factors affecting PCR-based estimates of microbial species richness and evenness

(2010) Anna Engelbrektson et al.   ISME Journal

Organismal, genetic, and transcriptional variation in the deeply sequenced gut microbiomes of identical twins

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

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

Molecular analyses reveal high levels of eukaryotic richness associated with enigmatic deep-sea protists (Komokiacea)

(2009) B. Lecroq et al.   Marine Biodiversity