Microbial 'omics


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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.

Tutorials

See the “tutorials” pull-down menu to learn what you can do with anvi’o.

Vignette

See all programs in anvi’o here: http://merenlab.org/software/anvio/vignette/

Citation

Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, Delmont TO. (2015) Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ 3:e1319

Please consider also citing the following paper if you are using the pangenomics / metapangenomics workflow:

Delmont TO and Eren AM. (2018) Linking pangenomes and metagenomes: the Prochlorococcus metapangenome. PeerJ 6:e4320

Blog posts on anvi’o and microbial ‘omics

Microbial 'Omics Workshop (Sun, Sep 09, 2018)

A light introduction to questions of microbial ecology and microbial omics through the story of crassphage

Installing anvi'o (Sun, Jun 26, 2016)

Instructions to install the v2 branch of the platform.

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.