Microbial 'omics


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anvi-interactive [program]

Start an anvi'o server for the interactive interface.

See program help menu or go back to the main page of anvi’o programs and artifacts.

Table of Contents

Provides

collection bin interactive svg

Requires or uses

profile-db single-profile-db contigs-db genes-db bin view-data dendrogram phylogeny

Usage

Anvi-interactive opens the Anvi’o interactive interface, which is one of the most sophisticated parts of Anvi’o.

The most widely-known view gives you beautiful concentric circles of data, but the interface has many forms and vast functionality, from manual metagenomic binning (check out anvi-interactive in a metagenomic workflow here) to examining various stats about your data. However, in case you don’t like circles, you can also display your data in a rectangle (as seen here).

In fact, the interface has many of its own blog posts, including a pretty comprehensive introductory tutorial here and a breakdown of its data types here.

Here, we’ll go through some things that the Anvi’o interactive interface is capable of through this program. More information about most of this can be found by calling anvi-interactive -h or by checking out the additional resources at the bottom of this page.

Running anvi-interactive on a profile database

One of the simplest ways to run the interactive interface (espeically useful for manual binning) is just providing a profile database and contigs database:

anvi-interactive -p profile-db \ -c contigs-db

For the central tree to display correctly, you’ll need to have run hierarchical clustering at some point while making your profile database (either during anvi-merge, or, if this is a single-profile-db, while running anvi-profile).

You’ll get lovely concentric circles (or rectangles), each filled with data that was contained in your databases and that you are now free to interact with. See the page for the interactive interface for more information.

Running on a specific collection

You can also run anvi-interactive on a specific collection. When doing this, Anvi’o will calculate various information about each of your bins, and display the interface. Each item of your central plot will not represent a contig, but a bin within your collection.

anvi-interactive -p profile-db \ -c contigs-db \ -C collection

Since clustering is done here, you can also customize the linkage method and distance metric if desired.

See the note on this mode in the metagenomic workflow for more information.

If instead you want to run the standard anvi’o interface, but only looking at contigs within a specific collection, use the tag --collection-autoload.

Looking at genes instead of bins or contigs

You can also start the interface in “gene mode,” in which each item of the central tree is a gene instead of a split or contig (or bin like in “collection mode”). A lot of the same functionality is availble, including looking at detection and coverage, Inspection, and sequence functionality. However, you cannot store states or collections in this mode.

Manual Inputs: I want to provide my own (non-Anvi’o) data!

You can do that with the flag --manual-mode and then by providing any of the following types of files:

  • a fasta file
  • a tab-delimited view data file
  • a NEWICK formatted tree
  • a flat file containing the order of the items you want to display

When doing this kind of run, if you don’t provide a profile database, Anvi’o will simply create an empty one for you.

Visualization Settings

In Anvi’o, the visualization settings at a given time are called a state.

To open the interface in a specific state, you can use the --state-autoload flag or by importing a state using anvi-import-state.

You can also customize various aspects of the interactive interface. For example, you can change the preselected view, title, and taxnomic level displayed (for example, showing the class name instead of the genus name). You can also hide outlier single nucleotide variations or open only a specific collection.

Adding additional information

You can add any additional layers of your choice using the parameter --additional-layers and providing a file containing the information you want to appear as another layer. You could also choose to split non-single-copy gene HMM hits into their own layer with the --split-hmm-layers parameter.

If you want to add an entirely new view to the interface, you can do that too, as long as you provide a file containing all split names and their associated values. For more information, see the parameter --additional-view.

You can also provide the manual inputs even if you’re using an Anvi’o database. For example, if you provide your own NEWICK formatted tree, you will have the option to display it instead of the one in your database.

Other things

Viewing your data

You can use this program to look at the available information in your databases, which is very convenient. For example, you can view all of the available

  • views (using --show-views)
  • states (using --show-states)
  • collections (using --list-collections)

Note for power users

You can also configure the server to your heart’s content, skip function call initizations, and change any of the output paths.

Edit this file to update this information.

Additional Resources

Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the __resources__ tag in this file to see an example.