Deriving accurate microbiota profiles from human samples with low bacterial content through post-sequencing processing of Illumina MiSeq data

Reagent and laboratory contamination can critically impact sequence-based microbiome analyses

(2014) Susannah J Salter et al.   BMC BIOLOGY

Assessment of quality control approaches for metagenomic data analysis

(2014) Qian Zhou et al.   Scientific Reports

Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients

(2014) Vladimir Lazarevic et al.   Frontiers in Cellular and Infection Microbiology

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Subsampled open-reference clustering creates consistent, comprehensive OTU definitions and scales to billions of sequences

(2014) Jai Ram Rideout et al.   PeerJ

The Effects of Airway Microbiome on Corticosteroid Responsiveness in Asthma

(2013) Elena Goleva et al.   AMERICAN JOURNAL OF RESPIRATORY AND CRITICAL CARE MEDICINE

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

(2013) J. Zhang et al.   BIOINFORMATICS

Microbial communities in the respiratory tract of patients with interstitial lung disease

(2013) Christian Garzoni et al.   THORAX

Enrichment of lung microbiome with supraglottic taxa is associated with increased pulmonary inflammation

(2013) Leopoldo N Segal et al.   Microbiome

New perspectives on viable microbial communities in low-biomass cleanroom environments

(2012) Parag Vaishampayan 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

Deep Sequencing Analyses of Low Density Microbial Communities: Working at the Boundary of Accurate Microbiota Detection

(2012) Giske Biesbroek et al.   PLoS One

Comparison of DNA Extraction Methods for Microbial Community Profiling with an Application to Pediatric Bronchoalveolar Lavage Samples

(2012) Dana Willner et al.   PLoS One

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea

(2011) Daniel McDonald et al.   ISME Journal

Fast Identification and Removal of Sequence Contamination from Genomic and Metagenomic Datasets

(2011) Robert Schmieder et al.   PLoS One

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

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