Integrated multi-omics at scale

An open-source, community-driven analysis and visualization platform for microbial 'omics.

Anvi'o in a nutshell

Anvi’o is a comprehensive platform that brings together many aspects of today’s cutting-edge computational strategies of data-enabled microbiology, including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.

The latest stable version of anvi’o is v7.1, and you can see the release notes here.

The platform stands on more than 200,000 lines of Python and JavaScript code that follow modern software development paradigms thanks to the voluntary contributions of more than 30 developers from the academia and industry to empower microbiologists for their complex needs through an architecture that enables reproducible science and simple interfaces for data access.

As a principle, anvi’o does not track its users by any means, but based on self-reported data on Twitter, there is at least one anvi’o user in the following countries:

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We welcome you to join in our growing international community, and we look forward to hearing from you. Please share your concerns, ideas, and feature requests with the anvi’o community, or ask your questions on microbial ‘omics on our group.

Funding and Support

Anvi’o is here thanks to the support from,

We were able to push the boundaries of anvi’o thanks to the funding we have received from,

  • Simons Foundation (2020-2022, via the Simons Early Career Investigator in Marine Microbial Ecology and Evolution Award to Meren).
  • Alfred P. Sloan Foundation (2020-2021, via the Fellowship in Ocean Sciences to Meren).
  • W. M. Keck Foundation (2018-2021, via the Microbiome dynamics and discovery through transfer RNA to Tao Pan, Meren, et al).

Learn anvi'o and more

Resources below cover a wide range of topics from most basic concepts to most advanced ones to help and inspire any scientist who studies microbial life through ‘omics (add more here or here).

Are you aware of a resource that should be here? Please let us know on or send us a pull request on GitHub by editing file.

Tutorials and exercises

Tutorials are the best way to start learning anvi’o. They typically use mock or simple datasets to describe basic concepts and how to accomplish common tasks in anvi’o often with hands-on experience.

An introduction to Unix Basics of the command line environment, the best friend of any scientist who wishes to work with data.
hands-on beginner
Basics of metagenomic read recruitment A very simple introduction to metagenomic read recruitment.
metagenomics theoretical beginner
A metagenomic read recruitment exercise A mini hands-on exercise is to conduct a simple read recruitment experiment with a mock dataset.
metagenomics hands-on beginner
The anvi'o pangenomics workflow A comprehensive description of the anvi'o pangenomics workflow.
pangenomics theoretical beginner
A pangenomics exercise A reproducible pangenomic analysis of seven Vibrio jascida genomes isolated in Woods Hole by the participants of Microbial Diversity Course.
pangenomics hands-on beginner
An exercise on single-cell genomics A hands-on tutorial to learn how to integrate single-cell genomics data into the anvi'o environment that covers the integration of SAGs into the anvi'o environment, performing pangenomic and phylogenomic analyses with them, and more.
pangenomics phylogenomics hands-on beginner
Anvi'o phylogenomics workflow A comprehensive description of the anvi'o phylogenomics workflow.
phylogenomics theoretical beginner
An exercise on metabolic reconstruction A hands-on exercise for the metabolism suite of programs in anvi’o. It starts with a section on how to estimate metabolism for a single bacterial isolate, and goes into larger, real-world dataset of metagenome-assembled genomes to demonstrate how to estimate metabolism compute enrichment scores for metabolic modules.
metabolism metabolic enrichment genomics metagenomics hands-on beginner
Anvi'o tools for microbial population genetics A theoretical tutorial describing how to characterize SNVs, SCVs and SAAVs with anvi’o, and how to interpret the output.
microbial population genetics theoretical intermediate
A primer on anvi'o with the Infant Gut Dataset A tutorial that walks you through some of the most fundamental aspects of anvi'o and its application to a real-world dataset organized in multiple interconnected chapters, which all use the same dataset.
metagenomics binning pangenomics phylogenomics microbial population genetics hands-on beginner
A metagenomics workshop featuring anvi'o Materials from a 2022 workshop on metagenomics in anvi'o, including read recruitment and metabolism estimation.
metagenomics metabolism hands-on beginner

Technical write-ups

Articles listed this section offer solutions or discussions regarding matters that are typically more technical than scientific (add more here).

Getting help from the anvi'o community A resource that describes how to find anvi'o programs and understand their utility, how to reach out to anvi'o community, and how to report technical problems.
beginner
Anvi'o interactive interface 101 A short tutorial that walks you through the capabilities of the anvi'o interactive interface using an intuitive dataset and _without_ using any of the actual anvi'o functionality.
interactive interface hands-on beginner
Anvi'o 'views' demystified Default data views in anvi'o intearctive interface
interactive interface theoretical beginner
Data types of anvi'o interactive interface a more detailed description of the interface by demonstrating the data types the interface can work with, and later details of the user interface.
interactive interface hands-on beginner
Running remote anvi'o interactive interfaces on your local computer A workaround to run anvi'o on a remote server, and display graphical user interfaces on your local browser seamlessly.
visualization server beginner
Combining multiple 'omics data types A workflow that describes how to combine metagenomics and metatrasncriptomics data appropriately.
metagenomics metatranscriptomics theoretical intermediate
Accessing and including NCBI genomes in 'omics analyses in anvi'o A tutorial that will walk you through the steps of downloading genomes of interest from the NCBI, processing NCBI GenBank files to get anvi’o compatible files, and running the anvi’o snakemake workflow for contigs to generate a contigs database for each of these genomes.
pangenomics hands-on intermediate
Extract loci from genomes and metagenomes with anvi'o A tutorial on how to use anvi-export-locus to target genomic regions of interest across genomes and/or metagenomic assemblies, and report sequences and/or anvi’o contigs databases for cut loci for downstream analyses.
genomics hands-on intermediate
Combining reference genome annotations with your own in pangenomes Demonstration of a way to incorporate new genomes with reference genomes from NCBI, while maintaining their vetted reference-genome annotations.
pangenomics hands-on intermediate
Importing VirSorter2 results into anvi'o A workflow (and a script) to import results from VirSorter2, a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses, into anvi'o databases as a collection of contigs
metagenomics viruses hands-on intermediate
Integrating AGNOSTOS gene categories into anvi'o projects A workflow to demonstrate how to import AGNOSTOS gene categories into anvi'o databases
metagenomics pangenomics hands-on advanced
Integrating sequence variants and predicted protein structures A theoretical tutorial describing the details of the structure database, how it’s created, and its utility.
structural biology microbial population genetics advanced

Articles, workflows, opinions

These resources often cover key insights into specific topics and can be useful to more advanced users and ‘omics enthusiasts in general.

The history of metagenomics: An incomplete summary An incomplete history of ideas that shpaped integrated genomics and metagenomics to explore microbial fitness in habitats such as the human gut and the oceans.
metagenomics beginner
Visualizing the fate of contigs across metagenomic binning algorithms A visual demonstration of the shortcomings of automatic binning of genomes from complex environments using short-read assemblies.
metagenomics binning beginner
Binning giant viruses and their close relatives A demonstration of how to reconstruct genomes of giant viruses.
metagenomics viruses binning intermediate
Targeted binning of a novel nitrogen-fixing population from the Arctic Ocean Using metabolism estimation to go fishing in some ocean metagenomes.
metagenomics binning metabolism
Inspecting the genomic link between Archaea and Eukaryota An easy-to-follow diary of resolving a composite Lokiarchaeum genome bin.
metagenomics binning beginner
An Akkermansia story with MinION long-reads An application of metagenomic long-read sequencing, assembly, correction, and the use of anvi'o pangenomics workflow to benchmark outcomes.
long-reads pangenomics theoretical intermediate
Welcome to the dark side of genomes and metagenomes A diary that shed light on the story and purpose of AGNOSTOS.
metagenomics pangenomics beginner
Estimating per-residue binding frequencies with InteracDome A technical diary for Evan's implementation of InteracDome into anvi'o.
structural biology microbial population genetics advanced