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

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

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

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

Qiita - A multi-omics databasing effort

Python package to study microbial communities using metabolic modeling.

DeepMicrobes: taxonomic classification for metagenomics with deep learning

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

Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

Woltka: a versatile meta'omic data classifier

Cross-disease comparison of case-control gut microbiome studies

Bioinformatics pipeline for recovery and analysis of metagenome-assembled genomes

Sample search by metadata and features

The Microbiome Interpretable Temporal Rule Engine

PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples

National Microbiome Data Collaborative (NMDC) unified data model

AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

creating hybrid-gene phylogenetic trees for diversity analyses