BiomMiner: An advanced exploratory microbiome analysis and visualization pipeline

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses

(2014) Pier Luigi Buttigieg et al.   FEMS MICROBIOLOGY ECOLOGY

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Enterotypes of the human gut microbiome

(2011) Manimozhiyan Arumugam et al.   NATURE

Metagenomic biomarker discovery and explanation

(2011) Nicola Segata et al.   GENOME BIOLOGY

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

Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples

(2009) James Robert White et al.   PLoS Computational Biology