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.

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

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
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

Meet anvi'o developers and contributors

A randomly ordered list of anvi’o developers and contributors.

Nick Youngblut Microbiologist studying methanogens and host-microbiome coevolution

Alon Shaiber Computational scientist previously studying microbial ecology, currently studying structural variation in cancer genomics, and what's next? Who knows?


Matthew Lawrence Klein Software developer interested in the role of technology in supporting a more equitable future on planet earth.

Emily Fogarty Microbiologist developing computational and wet lab strategies to study horizontal gene transfer in the human gut microbiome.

Jessica Pan Computer scientist interested in computational methods to investigate microbial ecosystems and making those techniques more accessible to others.


Daan R. Speth Microbiologist and bioinformatician interested in understanding the metabolic and phylogenetic diversity of microorganisms through genomics and wet lab analyses

Matthew Schechter Microbiologist interested in combining comparative genomics and environmental metagenomics to identify genetic determinants of fitness in microbial populations in the human gut and ocean microbiome.


Amy D. Willis Statistician and data scientist developing methods for the analysis of biodiversity, with a particular focus on the microbiome.

Antti Karkman Computational microbiologist interested in antibiotic resistance in the environment

Tom O. Delmont Microbial ecologist who seeks to understand small and large-scale ecological patterns in the microbial world.


Iva Veseli Computer scientist and biologist who leverages computational methods to study microbial metabolism in environmental metagenomes.

Jarrod J. Scott Microbiologist interested in understanding how bacteria and archaea coalesce into complex communities and how they affect host biology, biogeochemical cycles, and ecosystem-level processes in marine and terrestrial systems.

Andrea Watson Microbiologist interested in combining wet lab and computational methods in a complementary way to answer fundamental questions.

Isaac Fink Computer scientist interested in enhancing the power and accessibility of computational strategies to study microbial life.

Samuel Miller Computational and molecular microbiologist studying how microbes function in their environments through tRNA-sequencing, proteomics, and metagenomics.

Florian Trigodet Microbiologist using advanced computational strategies to make sense of the microbial ecology of complex habitats.

Mike Lee Bioinformatician who explores microbial ecology and evolution in a wide range of environments.


Evan Kiefl Computational biologist and software developer with a research focus on developing analysis and visualization strategies for complex multi-'omics data, particularly at the intersection of structural biology and metagenomics.

Xabier Vázquez-Campos Environmental microbiologist and bioinformatician - interested in all things 'omics, extremophiles, taxonomy and systematics, evolution...

Özcan C. Esen Computer engineer interested in developing tools for the visualization of complex data.

Simon Roux Viral ecologist and bioinformatician at the DOE JGI - interested in everything phage, 'omics, microbial and viral ecology and evolution, virus-host interactions, etc

Antonio Fernandez-Guerra Bioinformatician interested in development and application of new methodologies to analyze modern and ancient (meta)genomic data.

Quentin Clayssen Microbiologist and bioinformatician interested in metagenomics.


Mahmoud Yousef Computer scientist and medical student interested in exploring the intersection of bioinformatics and medicine, and how bioinformatic techniques can be used to advance the quality of medicine.

A. Murat Eren (Meren) Computer scientist and microbial ecologist interested in undersatnding mechanisms by which microbes interact with their surroundings, evolve, disperse, and respond to environmental change.

Jessika Fuessel Biogeochemist and microbiologist intereted in understanding the production and fate of microbial metabolites within the context of changing environmental conditions using a multi-omics.

How to cite anvi'o like a pro

Anvi’o is an evolving software ecosystem, and its components are often described in multiple studies. Thus, the best practice for your study may be to cite multiple publications if it benefits from multiple anvi’o features.

We know that finding the best studies to cite can be a lot of work. The purpose of this page is to offer up-to-date suggestions to help you find out how to finalize your citations regarding anvi’o. But if you are unsure, please feel free to drop us a line, or find us on

Anvi’o often uses third-party software or resources (such as HMMER, Prodigal, MCL, GTDB, or NCBI) and the platform typically guides you to cite relevant work when they are used for an anvi’o analysis. Suggestions on this page are specific to anvi’o, and do not include third-party software that you should also make sure to cite properly.

We know this is difficult work and we are thankful for your attention.

Default citation

If you have used anvi’o for anything at all please consider citing this work as it describes the software ecosystem in general which currently sits on more than 120,000 lines of code, which means any given anvi’o program benefits from the entirety of this ecosystem:

Community-led, integrated, reproducible multi-omics with anvi'o Eren AM, Kiefl E, Shaiber A, Veseli I, Miller SE, Schechter MS, Fink I, Pan JN, Yousef M, Fogarty EC, Trigodet F, Watson AR, Esen ÖC, Moore RM, Clayssen Q, Lee MD, Kivenson V, Graham ED, Merrill BD, Karkman A, Blankenberg D, Eppley JM, Sjödin A, Scott JJ, Vázquez-Campos X, McKay LJ, McDaniel EA, Stevens SLR, Anderson RE, Fuessel J, Fernandez-Guerra A, Maignien L, Delmont TO, Willis AD Nature Microbiology, 6(1):3:6 🔗

The rest of the citations on this page are specific for certain anvi’o features.

Functional enrichment analyses

This feature was described for the first time in this study:

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome Shaiber A, Willis AD, Delmont TO, Roux S, Chen L, Schmid AC, Yousef M, Watson AR, Lolans K, Esen ÖC, Lee STM, Downey N, Morrison HG, Dewhirst FE, Mark Welch JL, Eren AM Co-senior authors Genome Biology, 21:292 🔗

In a recent study, we cited this work the following way:

(…)

Functional enrichment analyses. The statistical approach for enrichment analysis is defined elsewhere (Shaiber et al. 2020), but briefly the program anvi-compute-functional-enrichment determined enrichment scores for functions (or metabolic modules) within groups of genomes by fitting a binomial generalized linear model (GLM) to the occurrence of each function (or complete metabolic module) in each group, and then computing a Rao test statistic, uncorrected p-values, and corrected q-values. We considered any function or metabolic module with a q-value less than 0.05 to be ‘enriched’ in its associated group (…)

Questions on enrichment analyses? You can ask

Snakemake workflows

There is not yet a published study that describes our workflows, although they were first introduced in the following work:

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome Shaiber A, Willis AD, Delmont TO, Roux S, Chen L, Schmid AC, Yousef M, Watson AR, Lolans K, Esen ÖC, Lee STM, Downey N, Morrison HG, Dewhirst FE, Mark Welch JL, Eren AM Co-senior authors Genome Biology, 21:292 🔗

In a recent study, we cited our workflows the following way:

(…)

‘Omics workflows. Whenever applicable, we automated and scaled our ‘omics analyses using the bioinformatics workflows implemented by the program anvi-run-workflow (Shaiber et al. 2020) in anvi’o (Eren et al. 2021). Anvi’o workflows implement numerous steps of bioinformatics tasks including short-read quality filtering, assembly, gene calling, functional annotation, hidden Markov model search, metagenomic read-recruitment, metagenomic binning, pangenomics, and phylogenomics. Workflows use Snakemake (Köster and Rahmann 2012) and a tutorial is available at the URL http://merenlab.org/anvio-workflows/. The following sections detail these steps.

(…)

Questions on anvi’o snakemake workflows? You can ask

Metabolic reconstruction

There is not yet a published study that describes anvi’o metabolic reconstruction capabilities, although in a recent study we mentioned the program we mentioned this framework the following way:

(…)

Analysis of metabolic modules and enrichment. We calculated the level of completeness for a given KEGG module (Kanehisa et al. 2014; Kanehisa et al. 2017) in our genomes using the program anvi-estimate-metabolism, which leveraged previous annotation of genes with KEGG orthologs (KOs) (see the section ‘Processing of contigs’). Then, the program anvi-compute-functional-enrichment determined whether a given metabolic module was enriched in based on the output from anvi-estimate-metabolism. The URL https://merenlab.org/m/anvi-estimate-metabolism serves a tutorial for this program which details the modes of usage and output file formats (…)

Questions on metabolism? You can ask

Single-amino acid variants

If you are using anvi’o to study microbial population genetics through single-codon or single-amino acid variants, please consider also citing this work:

Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade Delmont TO, Kiefl E, Kilinc O, Esen ÖC, Uysal I, Rappé MS, Giovannoni S, Eren AM Co-first authors eLife, 8:e46497 🔗

Questions on single-amino acid variants? You can ask

Metapangenomics

The metapangenomics was first introduced in this study. If you are using anvi’o to investigate how to bring together pangenomes and metagenomes, please consider citing this work as well.

Questions on metapangenomics? You can ask

Metagenomic binning / refinement

If you used anvi’o only for metagenomic binning or for the refinement of genomes, please consider citing this study, too.

Anvi’o: an advanced analysis and visualization platform for ‘omics data Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO PeerJ, 3:e1319 🔗

Questions on binning practices? You can ask