Ultrafast and accurate 16S rRNA microbial community analysis using Kraken 2

The Integrative Human Microbiome Project

(2019)   NATURE

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

(2019) Evan Bolyen et al.   NATURE BIOTECHNOLOGY

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

(2018) Alexandre Almeida et al.   GigaScience

Optimizing taxonomic classification of marker-gene amplicon sequences with QIIME 2’s q2-feature-classifier plugin

(2018) Nicholas A. Bokulich et al.   Microbiome

16S rRNA Next Generation Sequencing Analysis Shows Bacteria in Alzheimer’s Post-Mortem Brain

(2017) David C. Emery et al.   Frontiers in Aging Neuroscience

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

An evaluation of the accuracy and speed of metagenome analysis tools

(2016) Stinus Lindgreen et al.   Scientific Reports

The Dynamics of the Human Infant Gut Microbiome in Development and in Progression toward Type 1 Diabetes

(2015) Aleksandar D. Kostic et al.   Cell Host & Microbe

Diversity and Evolution in the Genome of Clostridium difficile

(2015) Daniel R. Knight et al.   CLINICAL MICROBIOLOGY REVIEWS

The Hidden World within Plants: Ecological and Evolutionary Considerations for Defining Functioning of Microbial Endophytes

(2015) Pablo R. Hardoim et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

Commensal Bifidobacterium promotes antitumor immunity and facilitates anti-PD-L1 efficacy

(2015) A. Sivan et al.   SCIENCE

The ocean sampling day consortium

(2015) Anna Kopf et al.   GigaScience

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Kraken: ultrafast metagenomic sequence classification using exact alignments

(2014) Derrick E Wood et al.   GENOME BIOLOGY

Structure and Functions of the Bacterial Microbiota of Plants

(2013) Davide Bulgarelli et al.   Annual Review of Plant Biology

Microbiota Modulate Behavioral and Physiological Abnormalities Associated with Neurodevelopmental Disorders

(2013) Elaine Y. Hsiao et al.   CELL

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

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

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data

(2012) Evguenia Kopylova et al.   BIOINFORMATICS

Structure, function and diversity of the healthy human microbiome

(2012)   NATURE

Cross-biome metagenomic analyses of soil microbial communities and their functional attributes

(2012) N. Fierer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrocarbon-Degrading Bacteria and the Bacterial Community Response in Gulf of Mexico Beach Sands Impacted by the Deepwater Horizon Oil Spill

(2011) Joel E. Kostka et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Soil bacterial and fungal communities across a pH gradient in an arable soil

(2010) Johannes Rousk et al.   ISME Journal

QIIME allows analysis of high-throughput community sequencing data

(2010) J Gregory Caporaso et al.   NATURE METHODS

Direct sequencing of the human microbiome readily reveals community differences

(2010) Justin Kuczynski et al.   GENOME 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

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS