Comparing bioinformatic pipelines for microbial 16S rRNA amplicon sequencing

Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

The Third Revolution in Sequencing Technology

(2018) Erwin L. van Dijk et al.   TRENDS IN GENETICS

Benchmarking taxonomic assignments based on 16S rRNA gene profiling of the microbiota from commonly sampled environments

(2018) Alexandre Almeida et al.   GigaScience

Depicting the composition of gut microbiota in a population with varied ethnic origins but shared geography

(2018) Mélanie Deschasaux et al.   NATURE MEDICINE

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

(2018) Jacob T. Nearing et al.   PeerJ

Cohort profile: the Healthy Life in an Urban Setting (HELIUS) study in Amsterdam, The Netherlands

(2017) Marieke B Snijder et al.   BMJ Open

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

(2017) Robert C. Edgar   PeerJ

OptiClust, an Improved Method for Assigning Amplicon-Based Sequence Data to Operational Taxonomic Units

(2017) Sarah L. Westcott et al.   mSphere

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

The Human Intestinal Microbiome in Health and Disease

(2016) Susan V. Lynch et al.   NEW ENGLAND JOURNAL OF MEDICINE

VSEARCH: a versatile open source tool for metagenomics

(2016) Torbjørn Rognes et al.   PeerJ

Error filtering, pair assembly and error correction for next-generation sequencing reads

(2015) Robert C. Edgar et al.   BIOINFORMATICS

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

(2014) Jai Ram Rideout et al.   PeerJ

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

(2013) James J. Kozich et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

UPARSE: highly accurate OTU sequences from microbial amplicon reads

(2013) Robert C Edgar   NATURE METHODS

phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data

(2013) Paul J. McMurdie et al.   PLoS One

Biomonitoring 2.0: a new paradigm in ecosystem assessment made possible by next-generation DNA sequencing

(2012) DONALD J. BAIRD et al.   MOLECULAR ECOLOGY

VennDiagram: a package for the generation of highly-customizable Venn and Euler diagrams in R

(2011) Hanbo Chen et al.   BMC BIOINFORMATICS

Sequence-specific error profile of Illumina sequencers

(2011) Kensuke Nakamura et al.   NUCLEIC ACIDS RESEARCH

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