Development of a Dual-Index Sequencing Strategy and Curation Pipeline for Analyzing Amplicon Sequence Data on the MiSeq Illumina Sequencing Platform

Microbial phylogenetic profiling with the Pacific Biosciences sequencing platform

(2013) Erin B Fichot et al.   Microbiome

PANDAseq: paired-end assembler for illumina sequences

(2012) Andre P Masella et al.   BMC BIOINFORMATICS

Secondary structure improves OTU assignments of 16S rRNA gene sequences

(2012) Patrick D Schloss   ISME Journal

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

(2012) J Gregory Caporaso et al.   ISME Journal

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing

(2012) Nicholas A Bokulich et al.   NATURE METHODS

Bacterial Community Shift in Treated Periodontitis Patients Revealed by Ion Torrent 16S rRNA Gene Amplicon Sequencing

(2012) Sebastian Jünemann et al.   PLoS One

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

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

Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys

(2011) Jeffrey J Werner et al.   ISME Journal

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

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

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

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

Microbiome Profiling by Illumina Sequencing of Combinatorial Sequence-Tagged PCR Products

(2010) Gregory B. Gloor et al.   PLoS One

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

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

ABySS: A parallel assembler for short read sequence data

(2009) J. T. Simpson et al.   GENOME RESEARCH

A High-Throughput DNA Sequence Aligner for Microbial Ecology Studies

(2009) Patrick D. Schloss   PLoS One

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE