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
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
Fast taxonomic classification of metagenomic sequencing reads using a protein reference database
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
Assembly and binning of metagenomes
🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.
Genomic Data Retrieval with R
CAMISIM: Simulating metagenomes and microbial communities
Amplicon sequencing analysis workflow using DADA2 and QIIME2