Microbial 'omics

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interactive [artifact]

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A DISPLAY-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..

Back to the main page of anvi’o programs and artifacts.

Provided by

anvi-3dev anvi-display-contigs-stats anvi-display-metabolism anvi-display-pan anvi-inspect anvi-interactive anvi-script-snvs-to-interactive

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This page describes the many interactive interfaces that are utilized in Anvi’o. The most well-known and sophisticated of these are the beautiful concentric circles (though they can also be displayed in other shapes) given by anvi-interactive and anvi-display-pan.

If you’re new to the anvi’o interactive interface, you’ll probably want to check out this tutorial for beginners or the other resources on the anvi-interactive page.

However, there are more interfaces availible in anvi’o than just that one, so let’s list them out:

  • anvi-3dev lets you examine specific protein strcutures, along with SCV and SAAVs within it. (It even has its own software page.. It’s kind of a big deal.)

  • anvi-display-contigs-stats shows you various stats about the contigs within a contigs-db, such as their hmm-hits, lengths, N and L statistics, and so on.

  • anvi-display-metabolism is still under development but will allow you to interactively view metabolism estimation data using anvi-estimate-metabolism under the hood.

  • anvi-display-pan displays information about the gene clusters that are stored in a pan-db. It lets you easily view your core and accessory genes, and can even be turned into a metapangenome through importing additional data tables.

  • anvi-inspect lets you look at a single split across your samples, as well as the genes identified within it. This interface can also be opened from the anvi-interactive interface by asking for details about a specific split.

  • anvi-interactive displays the information in a profile-db. It lets you view the distribution of your contigs across your samples, manually bin metagenomic data into MAGSs (and refine those bins with anvi-refine), and much more. You can also use this to look at your genes instead of your contigs or examine the genomes after a phylogenomic anlysis. Just look at that program page for a glimpse of this program’s amazingness.

  • anvi-script-snvs-to-interactive lets you view a comprehensive summary of the SNVs, SCVs, and SAAVs within your contigs.

Edit this file to update this information.