microbiome

Versatile open-source tool for microbiome analysis

Accurate sample inference from amplicon data with single nucleotide resolution

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

microbiome R package

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

💎 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

Nature Communications | BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data

Make Picrust2 Output Analysis and Visualization Easier

R package for microbiome biomarker discovery

🦠 A comprehensive R package for deep mining microbiome

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

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

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

Human Microbiome wiki

MaAsLin2: Microbiome Multivariate Association with Linear Models

A robust and fast clustering method for amplicon-based studies

Kun-peng: an ultra-fast, low-memory footprint and accurate taxonomy classifier for all

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

PANDORA 💻