NG-Tax 2.0: A Semantic Framework for High-Throughput Amplicon Analysis

The Empusa code generator and its application to GBOL, an extendable ontology for genome annotation

(2019) Jesse C. J. van Dam et al.   Scientific Data

Updating the 97% identity threshold for 16S ribosomal RNA OTUs

(2018) Robert C Edgar   BIOINFORMATICS

Best practices for analysing microbiomes

(2018) Rob Knight et al.   NATURE REVIEWS MICROBIOLOGY

Indel-correcting DNA barcodes for high-throughput sequencing

(2018) John A. Hawkins et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Madness of Microbiome: Attempting To Find Consensus “Best Practice” for 16S Microbiome Studies

(2018) Jolinda Pollock et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

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

(2017) Benjamin J Callahan et al.   ISME Journal

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

(2016) Melanie Schirmer et al.   BMC BIOINFORMATICS

Characterization of sequence-specific errors in various next-generation sequencing systems

(2016) Sunguk Shin et al.   Molecular BioSystems

Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies

(2016) Daryl M Gohl et al.   NATURE BIOTECHNOLOGY

DADA2: High-resolution sample inference from Illumina amplicon data

(2016) Benjamin J Callahan et al.   NATURE METHODS

Synthetic spike-in standards for high-throughput 16S rRNA gene amplicon sequencing

(2016) Dieter M. Tourlousse et al.   NUCLEIC ACIDS RESEARCH

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

An assessment of US microbiome research

(2016) Elizabeth Stulberg et al.   Nature Microbiology

A new view of the tree of life

(2016) Laura A. Hug et al.   Nature Microbiology

mockrobiota: a Public Resource for Microbiome Bioinformatics Benchmarking

(2016) Nicholas A. Bokulich et al.   mSystems

A perspective on 16S rRNA operational taxonomic unit clustering using sequence similarity

(2016) Nam-Phuong Nguyen et al.   npj Biofilms and Microbiomes

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

Interpreting 16S metagenomic data without clustering to achieve sub-OTU resolution

(2014) Mikhail Tikhonov et al.   ISME Journal

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

(2014) Pablo Yarza et al.   NATURE REVIEWS MICROBIOLOGY

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

The SILVA and “All-species Living Tree Project (LTP)” taxonomic frameworks

(2013) Pelin Yilmaz et al.   NUCLEIC ACIDS RESEARCH

The Long-Term Stability of the Human Gut Microbiota

(2013) J. J. Faith et al.   SCIENCE

The SILVA ribosomal RNA gene database project: improved data processing and web-based tools

(2012) Christian Quast 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

Matrix correlations for high-dimensional data: the modified RV-coefficient

(2008) A. K. Smilde et al.   BIOINFORMATICS