Effects of OTU Clustering and PCR Artifacts on Microbial Diversity Estimates

Which sequencing depth is sufficient to describe patterns in bacterial α- and β-diversity?

(2012) Daniel Lundin et al.   Environmental Microbiology Reports

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

Removing Noise From Pyrosequenced Amplicons

(2011) Christopher Quince et al.   BMC BIOINFORMATICS

Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons

(2011) B. J. Haas et al.   GENOME RESEARCH

Illumina-based analysis of microbial community diversity

(2011) Patrick H Degnan et al.   ISME Journal

Robust Computational Analysis of rRNA Hypervariable Tag Datasets

(2011) Maksim Sipos et al.   PLoS One

Sampling and pyrosequencing methods for characterizing bacterial communities in the human gut using 16S sequence tags

(2010) Gary D Wu et al.   BMC MICROBIOLOGY

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

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

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

(2010) Anna Engelbrektson et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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

Comparison of Species Richness Estimates Obtained Using Nearly Complete Fragments and Simulated Pyrosequencing-Generated Fragments in 16S rRNA Gene-Based Environmental Surveys

(2009) N. Youssef 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

Unique archaeal assemblages in the Arctic Ocean unveiled by massively parallel tag sequencing

(2009) Pierre E Galand et al.   ISME Journal

SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building

(2009) M. Gouy et al.   MOLECULAR BIOLOGY AND EVOLUTION

The 'rare biosphere': a reality check

(2009) Jens Reeder et al.   NATURE METHODS

Accurate determination of microbial diversity from 454 pyrosequencing data

(2009) Christopher Quince et al.   NATURE METHODS

Topographical and Temporal Diversity of the Human Skin Microbiome

(2009) E. A. Grice et al.   SCIENCE

Quality scores and SNP detection in sequencing-by-synthesis systems

(2008) W. Brockman et al.   GENOME RESEARCH