Toward accurate molecular identification of species in complex environmental samples: testing the performance of sequence filtering and clustering methods

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

(2014) Ali May et al.   BIOINFORMATICS

A molecular-based approach for examining responses of eukaryotes in microcosms to contaminant-spiked estuarine sediments

(2014) Anthony A. Chariton et al.   ENVIRONMENTAL TOXICOLOGY AND CHEMISTRY

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

Swarm: robust and fast clustering method for amplicon-based studies

(2014) Frédéric Mahé et al.   PeerJ

M-pick, a modularity-based method for OTU picking of 16S rRNA sequences

(2013) Xiaoyu Wang et al.   BMC BIOINFORMATICS

MSClust: A Multi-Seeds based Clustering algorithm for microbiome profiling using 16S rRNA sequence

(2013) Wei Chen et al.   JOURNAL OF MICROBIOLOGICAL METHODS

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

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

(2013) Elianne Egge et al.   PLoS One

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

(2013) Wei Chen et al.   PLoS One

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

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

Comparing clustering and pre-processing in taxonomy analysis

(2012) Marc J. Bonder et al.   BIOINFORMATICS

Accuracy of protist diversity assessments: morphology compared with cloning and direct pyrosequencing of 18S rRNA genes and ITS regions using the conspicuous tintinnid ciliates as a case study

(2012) Charles Bachy et al.   ISME Journal

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast et al.   NUCLEIC ACIDS RESEARCH

Two-Stage Clustering (TSC): A Pipeline for Selecting Operational Taxonomic Units for the High-Throughput Sequencing of PCR Amplicons

(2012) Xiao-Tao Jiang et al.   PLoS One

Testing three pipelines for 18S rDNA-based metabarcoding of soil faunal diversity

(2012) ChenXue Yang et al.   Science China-Life Sciences

Sequencing our way towards understanding global eukaryotic biodiversity

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

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

A grammar-based distance metric enables fast and accurate clustering of large sets of 16S sequences

(2011) David J Russell et al.   BMC BIOINFORMATICS

DNACLUST: accurate and efficient clustering of phylogenetic marker genes

(2011) Mohammadreza Ghodsi et al.   BMC BIOINFORMATICS

Estimation of bacterial diversity using next generation sequencing of 16S rDNA: a comparison of different workflows

(2011) Jorge Barriuso et al.   BMC BIOINFORMATICS

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

A large-scale benchmark study of existing algorithms for taxonomy-independent microbial community analysis

(2011) Y. Sun et al.   BRIEFINGS IN BIOINFORMATICS

Who is eating what: diet assessment using next generation sequencing

(2011) FRANCOIS POMPANON et al.   MOLECULAR ECOLOGY

ESPRIT-Tree: hierarchical clustering analysis of millions of 16S rRNA pyrosequences in quasilinear computational time

(2011) Yunpeng Cai et al.   NUCLEIC ACIDS RESEARCH

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

SeqTrim: a high-throughput pipeline for preprocessing any type of sequence reads

(2010) Juan Falgueras et al.   BMC BIOINFORMATICS

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

(2010) Anke Behnke et al.   ENVIRONMENTAL MICROBIOLOGY

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

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

A Clustering Optimization Strategy for Molecular Taxonomy Applied to Planktonic Foraminifera SSU rDNA

(2010) Markus Göker et al.   Evolutionary Bioinformatics

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

454 Pyrosequencing and Sanger sequencing of tropical mycorrhizal fungi provide similar results but reveal substantial methodological biases

(2010) Leho Tedersoo et al.   NEW PHYTOLOGIST

Second-generation environmental sequencing unmasks marine metazoan biodiversity

(2010) Vera G. Fonseca et al.   Nature Communications

The Effects of Alignment Quality, Distance Calculation Method, Sequence Filtering, and Region on the Analysis of 16S rRNA Gene-Based Studies

(2010) Patrick D. Schloss   PLoS Computational Biology

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

Repetitive sequence variation and dynamics in the ribosomal DNA array of Saccharomyces cerevisiae as revealed by whole-genome resequencing

(2009) S. A. James et al.   GENOME RESEARCH

Next-generation gap

(2009) John D McPherson   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

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

(2009) Yijun Sun et al.   NUCLEIC ACIDS RESEARCH

The Ribosomal Database Project: improved alignments and new tools for rRNA analysis

(2008) J. R. Cole et al.   NUCLEIC ACIDS RESEARCH