MMseqs2: ultra fast and sensitive search and clustering suite

Versatile open-source tool for microbiome analysis

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

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

Accurate sample inference from amplicon data with single nucleotide resolution

An analysis and visualization platform for 'omics data

A complete pipeline for metagenomic analysis

ATLAS - Three commands to start analyzing your metagenome data

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

A collection of Galaxy-related training material

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

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

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

Assembly and binning of metagenomes

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

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

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

Genomic Data Retrieval with R

Amplicon sequencing analysis workflow using DADA2 and QIIME2