Denoising the Denoisers: an independent evaluation of microbiome sequence error-correction approaches

Multi-omics differentially classify disease state and treatment outcome in pediatric Crohn’s disease

(2018) Gavin M. Douglas et al.   Microbiome

Exact sequence variants should replace operational taxonomic units in marker-gene data analysis

(2017) Benjamin J Callahan et al.   ISME Journal

Accuracy of microbial community diversity estimated by closed- and open-reference OTUs

(2017) Robert C. Edgar   PeerJ

Microbiome Helper: a Custom and Streamlined Workflow for Microbiome Research

(2017) André M. Comeau et al.   mSystems

Moderate Exercise Has Limited but Distinguishable Effects on the Mouse Microbiome

(2017) Emily V. Lamoureux et al.   mSystems

Deblur Rapidly Resolves Single-Nucleotide Community Sequence Patterns

(2017) Amnon Amir et al.   mSystems

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

(2016) Nicholas A. Bokulich et al.   mSystems

Expanding the UniFrac Toolbox

(2016) Ruth G. Wong et al.   PLoS One

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

(2013) J. Zhang et al.   BIOINFORMATICS

Towards a unified paradigm for sequence-based identification of fungi

(2013) Urmas Kõljalg et al.   MOLECULAR ECOLOGY

Ribosomal Database Project: data and tools for high throughput rRNA analysis

(2013) James R. Cole et al.   NUCLEIC ACIDS RESEARCH

UCHIME improves sensitivity and speed of chimera detection

(2011) Robert C. Edgar et al.   BIOINFORMATICS

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

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