Estimating per-residue binding frequencies with InteracDome (Wed, Jul 22, 2020)
A blog post detailing InteracDome's integration into anvi'o
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.
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.
See our community resources, or browse all anvi’o programs and artifacts.
See the “tutorials” pull-down menu to learn what you can do with anvi’o.
Thank you for citing anvi’o from your work! Please take moment to visit this page to figure out how to do that best.
A blog post detailing InteracDome's integration into anvi'o
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Mike Lee heroically combines reference annotations with new annotations
A light introduction to questions of microbial ecology and microbial omics through the story of crassphage
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Details of a beautiful algorithm.
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Use anvi'o to get rRNA genes out of single-cells, clultivars, metagenome-assembled genomes, or even from entire metagenomic assemblies because why not.
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A resource to find out whether we are coming to or you just missed an event close to a location near you.
Instructions to install the current release of the platform.
Sweets for people who managed to install the platform and want to do genome-resolved metagenomics.
Recipes to install various software tools anvi'o uses
Various ways to add the taxonomic annotations into anvi'o
Making those functions in the summary output bloom with stuff!
So you have an assembly, or a draft genome, or a MAG, but no metagenomic short reads? That's OK.
Mike Lee demonstrates how to use a custom HMM single-copy gene profile for archaeal genomes
Data types, usage tips, and other stuff about the interface
Musings over a *Nitrospira* genome that can do complete nitrification
A quick way to get an insight into the number of genomes your contigs represent.
For people who does not have time to download stuff.
The user-friendly interface anvi'o provides to work with pangenomes.
Fresh anvi'o builds for the lazy.
Do you want to try anvi'o? Do you have a MAC computer? We got you covered.
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Anvi'o provides an interface to screen for possible contaminants and curate individual genomes
Bowtie, Bowtie2, BWA, CLC, GSNAP, BBMap, Novoalign, and SMALT.
Tricks for people who like to go deeper.
Dealing with heavily contaminated bins identified in an unsupervised manner.
Sweets for people who managed to install the platform.
Instructions to install the v1 brach of the platform.