Versatile open-source tool for microbiome analysis

Accurate sample inference from amplicon data with single nucleotide resolution

microbiome R package

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

Amplicon sequencing analysis workflow using DADA2 and QIIME2

🦠 A comprehensive R package for deep mining microbiome

R package for microbiome biomarker discovery

Human Microbiome wiki

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

PANDORA 💻

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

A robust and fast clustering method for amplicon-based studies

MaAsLin2: Microbiome Multivariate Association with Linear Models

Qiita - A multi-omics databasing effort

Make Picrust2 Output Analysis and Visualization Easier

Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.