Estimating per-residue binding frequencies with InteracDome (Wed, Jul 22, 2020)
A blog post detailing InteracDome's integration into anvi'o
Table of Contents
Anvi’o: integrated multi-omics at scale
Anvi’o is an open-source, community-driven analysis and visualization platform for microbial ‘omics. It brings together many aspects of today’s cutting-edge strategies including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in an integrated and easy-to-use fashion through extensive interactive visualization capabilities.
Anvi’o currently stands on more than 80,000 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, empowering 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 look forward to hearing from you. Share your concerns, ideas, and feature requests with the anvi’o community, or ask your questions on microbial ‘omics through any of our online venues.
Questions? Concerns? Find us on 
Install
Installing anvi’o is quite straightforward on Mac, Linux, or Windows operating systems. Following our installation tutorial you can install the latest stable version of anvi’o or tap into our master code repository to track the very latest changes. Alternatively, you can use one of our Docker containers without any installation.
Get Help
See our community resources, or browse all anvi’o programs and artifacts.
Tutorials
See the “tutorials” pull-down menu to learn what you can do with anvi’o.
Citation
Thank you for citing anvi’o from your work! Please take moment to visit this page to figure out how to do that best.
Blog posts on anvi’o and microbial ‘omics
Visualizing contig coverages to better understand microbial population structures (Mon, Nov 25, 2019)
Ways to visualize mapping results in anvi'o to make informed statements about environmental populations and to generate high-quality figures)
Extract loci from genomes and metagenomes with anvi'o (Thu, Oct 17, 2019)
A flexible and scalable approach to locate and extract target genetic loci from larger genetic contexts.
Genome / metagenome / MAG taxonomy with anvi'o (Tue, Oct 08, 2019)
An attempt at alchemy combining the magic of GTDB and single-copy core genes in anvi'o.
Getting help from the anvi'o community (Mon, Oct 07, 2019)
A primer on how to find your way through the maze of microbial 'omics and anvi'o
Accessing and including NCBI genomes in 'omics analyses in anvi'o (Thu, Mar 14, 2019)
How to download, process, and combine genomes from NCBI in your phylogenomic, pangenomic, and/or other 'omics analyses
Combining reference genome annotations with your own in pangenomes (Sat, Dec 01, 2018)
Mike Lee heroically combines reference annotations with new annotations
Microbial 'Omics Workshop (Sun, Sep 09, 2018)
A light introduction to questions of microbial ecology and microbial omics through the story of crassphage
Integrating sequence variants and predicted protein structures (Tue, Sep 04, 2018)
A discussion on the practical and theoretical aspects of using anvi'o structure
Anvi'o snakemake workflows (Mon, Jul 09, 2018)
Bringing the magic of anvi'o together with the wonders of snakemake.
Assessing the completion of eukaryotic bins with anvi'o (Sat, May 05, 2018)
A preliminary set of 83 HMMs from BUSCO. -Lol is anvi'o doing picoeuks now fam? -Why yes, yes it does.
Running remote anvi'o interactive interfaces on your local computer (Wed, Mar 07, 2018)
A hacker's guide to anvi'o networking. Are you scared? You should be!
Amino acid color coding by conservation in anvi'o gene clusters (Tue, Feb 13, 2018)
Details of a beautiful algorithm.
Importing VirSorter annotations into anvi'o to study phages (Thu, Feb 08, 2018)
Anvi'o projects meet the underappreciated owners of this planet.
Importing GhostKOALA/KEGG annotations into anvi'o (Wed, Jan 17, 2018)
KEGG modules, meet anvi'o. Anvi'o, meet KEGG modules.
Working with anvi'o additional data tables (Mon, Dec 11, 2017)
Getting additional data in an out of pan and profile databases like a pro.
Recovering ribosomal RNA gene sequences with anvi'o (Sun, Jul 09, 2017)
Use anvi'o to get rRNA genes out of single-cells, clultivars, metagenome-assembled genomes, or even from entire metagenomic assemblies because why not.
An anvi'o workflow for phylogenomics (Wed, Jun 07, 2017)
That is easy, but not simple
Importing Prokka annotations into anvi'o (Thu, May 18, 2017)
If Prokka doesn't come to you, you go to Prokka
The new anvi'o 'news' tab (Tue, May 16, 2017)
Is the big brother watching you? If he does, what does he see?
Notes on genome refinement with anvi'o (Thu, May 11, 2017)
More than just completion and redundancy estimates
Anvi'o 'views' demystified (Mon, May 08, 2017)
Mike Lee heroically demystifies the view options
The new anvi'o BAM profiler (Tue, Mar 07, 2017)
Has decades of suffering of thousands of anvi'o users come to an end?
An anvi'o workflow for microbial pangenomics (Tue, Nov 08, 2016)
The user-friendly interface anvi'o provides to work with pangenomes.
Working with SVG files anvi'o generate (Thu, Oct 27, 2016)
In other words, not putting screenshots in papers
Annotating an anvi'o contigs database with COGs (Tue, Oct 25, 2016)
Yes. Good ol' COGs. Into your contigs db. Just like that. 60% of the time, every time.
Microbial 'omics and anvi'o workshops (Thu, Aug 18, 2016)
A resource to find out whether we are coming to or you just missed an event close to a location near you.
Installing anvi'o (Sun, Jun 26, 2016)
Instructions to install the current release of the platform.
Anvi'o User Tutorial for Metagenomic Workflow (Wed, Jun 22, 2016)
Sweets for people who managed to install the platform and want to do genome-resolved metagenomics.
Installing third-party software (Sat, Jun 18, 2016)
Recipes to install various software tools anvi'o uses
Importing taxonomy into contigs database (Sat, Jun 18, 2016)
Various ways to add the taxonomic annotations into anvi'o
Importing functions into contigs database (Sat, Jun 18, 2016)
Making those functions in the summary output bloom with stuff!
Binning without mapping (Mon, Jun 06, 2016)
So you have an assembly, or a draft genome, or a MAG, but no metagenomic short reads? That's OK.
Making anvi'o use your own HMM collection (Sat, May 21, 2016)
Mike Lee demonstrates how to use a custom HMM single-copy gene profile for archaeal genomes
The anvi'o interactive interface (Sat, Feb 27, 2016)
Data types, usage tips, and other stuff about the interface
A short journey into a metagenomic dataset (Wed, Dec 09, 2015)
Musings over a *Nitrospira* genome that can do complete nitrification
How many bacterial genomes do you have in that assembly? (Mon, Dec 07, 2015)
A quick way to get an insight into the number of genomes your contigs represent.
Running the interactive interface through an SSH tunnel (Sat, Nov 28, 2015)
For people who does not have time to download stuff.
An anvi'o workflow for microbial pangenomics (old version) (Sat, Nov 14, 2015)
The user-friendly interface anvi'o provides to work with pangenomes.
Docker image for anvi'o (Sat, Aug 22, 2015)
Fresh anvi'o builds for the lazy.
OS X installer for anvi'o (Thu, Aug 20, 2015)
Do you want to try anvi'o? Do you have a MAC computer? We got you covered.
Studying microbial population genetics with anvi'o (Mon, Jul 20, 2015)
Exploring micro-diversity patterns using for deeper insights into ecology
Removing contaminants from cultivars with anvi'o (Thu, Jun 25, 2015)
Anvi'o provides an interface to screen for possible contaminants and curate individual genomes
Comparing different mapping software using anvi'o (Tue, Jun 23, 2015)
Bowtie, Bowtie2, BWA, CLC, GSNAP, BBMap, Novoalign, and SMALT.
Combining metagenomics with metatranscriptomics (Wed, Jun 10, 2015)
Tricks for people who like to go deeper.
Refining a bin using anvi'o (Mon, May 11, 2015)
Dealing with heavily contaminated bins identified in an unsupervised manner.
Anvi'o User Tutorial for Metagenomic Workflow (v1) (Sat, May 02, 2015)
Sweets for people who managed to install the platform.
Installing anvi'o (v1) (Fri, May 01, 2015)
Instructions to install the v1 brach of the platform.