MMseqs2: ultra fast and sensitive search and clustering suite

Versatile open-source tool for microbiome analysis

Ultra-fast and memory-efficient (meta-)genome assembler

Accurate sample inference from amplicon data with single nucleotide resolution

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

An analysis and visualization platform for 'omics data

ATLAS - Three commands to start analyzing your metagenome data

A complete pipeline for metagenomic analysis

A collection of Galaxy-related training material

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Rapid comparison and dereplication of genomes

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

🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results

Genomic Data Retrieval with R

Assembly and binning of metagenomes

🚀 A sequencing simulator

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic metagenomics

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