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
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.
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