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

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

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

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

CAMISIM: Simulating metagenomes and microbial communities

🚀 A sequencing simulator

A robust, extensible metagenomics pipeline

SemiBin: metagenomics binning with self-supervised deep learning

Rapid Profiling and Deconvolution Tool for Metagenomes

A utility for easy downloading of reads from next-gen sequencing repositories like NCBI SRA

ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more

A hybrid assembly and MAG recovery pipeline (and more!)

DeepMicrobes: taxonomic classification for metagenomics with deep learning

Recentrifuge: robust comparative analysis and contamination removal for metagenomics

✨🧬 Refined binning of metagenomic contigs using assembly graphs

A package for designing compact and comprehensive capture probe sets.

A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes