Microbial 'omics


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anvi-script-snvs-to-interactive [program]

Table of Contents

Take the output of anvi-gen-variability-profile, prepare an output for interactive interface.

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

Can provide

interactive

Can consume

variability-profile-txt

Usage

This programs takes a variability-profile-txt and generates the information necessary to visualize its contents with anvi-interactive.

Specifically, this program outputs a directory that contains a profile-db, a view-data artifact, and a dendrogram. For example, if you ran this program like so:

anvi-script-snvs-to-interactive -o OUTPUT_DIR \ variability-profile

Then, you can open the interactive interface by running

anvi-interactive --manual-mode \ -p OUTPUT_DIR/profile.db \ --tree OUTPUT_DIR/tree.txt \ --view-data OUTPUT_DIR/view.txt

Other parameters

Using Only a Subset of the Input

By default, all variability positions in your variability profile are considered. However, if the input is too large (i.e. more than 25,000 variability positions), the runtime on this program will be very long and the results won’t display well. So, there are several ways to remove variability positions from the input to get under this threshold:

  1. Ignore positions with with certain departures from the consensus sequence (with --min-departure-from-consensus and --max-departure-from-consensus)
  2. Ignore positions with with certain departures from the reference sequence (with --min-departure-from-reference and --max-departure-from-reference)
  3. Ignore positions in all non-coding regions with the flag --only-in-genes.

If you still have more positions than you can tell the program to pick a random subset of the input with the parameter --random followed by a seed integer.

Modifying the Output

By the default, the output data will use the departure from consensus values. If instead you want to look at the departure from the reference, just add the falg --display-dep-from-reference

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.