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

Quickly search, compare, and analyze genomic and metagenomic data sets.

An analysis and visualization platform for 'omics data

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

🌈 Interactive analysis of metagenomics data

A complete pipeline for metagenomic analysis

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

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

Read alignment statistics for metagenomics

A collection of Galaxy-related training material

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

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

Variational autoencoder for metagenomic binning

GENERanno: A Genomic Foundation Model for Metagenomic Annotation

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

Classifier for metagenomic sequences

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

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

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

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

CAMISIM: Simulating metagenomes and microbial communities