Microbial 'omics


Brought to you by

anvi-rename-bins [program]

Rename all bins in a given collection (so they have pretty names).

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

Table of Contents

Provides

collection bin

Requires or uses

collection bin profile-db contigs-db

Usage

This program creates a new collection from the bins in another collection with specific guidelines. This is especially helpful when you want to merge multiple collections later or share your project with someone, and you want all of your bins to have nicer names than the default bin_01, bin_02, etc. based on the order you binned them in.

So let’s take a look at what this program can do with a simple example.

Example 1: Renaming all bins in a collection

Let’s say you have a collection called MY_COLLECTION, which has four bins: really, bad, bin, and names. These names just won’t do, so let’s get to renaming. To rename all of my bins and put them into a collection called SURFACE_OCEAN_SAMPLES, you could run

anvi-rename-bins -c contigs-db \ -p profile-db \ --prefix SURFACE_OCEAN \ --collection-to-read MY_COLLECTION \ --collection-to-write SURFACE_OCEAN_SAMPLES \ --report-file rename.txt

And voila! Now you have a second collection named SURFACE_OCEAN_SAMPLES that contains your four bins, now named SURFACE_OCEAN_Bin_00001, SURFACE_OCEAN_Bin_00002, SURFACE_OCEAN_Bin_00003, and SURFACE_OCEAN_Bin_00004. The order that the numbers are in represents the quality of the bin as a MAG, given by the completion minus redunancy.

The file rename.txt is just a tab-delimited file that contains a summary of your renaming process. The first column has the original name of the bins that you renamed, the second has their new names, and the remaining columns contain information about those bins (like their completion, redundency, and size).

Example 2: Separating out the MAGs

Okay, but what if you want to label your MAGs separately from your bins? You don’t like SURFACE_OCEAN_bin_00004 since it only has a completition stat of 50 percent, and you’re not sure if you want to include SURFACE_OCEAN_bin_00003 since it has 50 percent redundency. How can you differenciate these iffy bins in your collection?

Here is the solution:

anvi-rename-bins -c contigs-db \ -p profile-db \ --prefix SURFACE_OCEAN \ --collection-to-read MY_COLLECTION \ --collection-to-write SURFACE_OCEAN_MAGS \ --report-file rename.txt \ --call-MAGs \ --min-completition-for-MAG 70

Now, the collection SURFACE_OCEAN_MAGS will include SURFACE_OCEAN_MAG_00001, SURFACE_OCEAN_MAG_00002, SURFACE_OCEAN_MAG_00003, and SURFACE_OCEAN_Bin_00004. These are exactly the same bins that the collection contained before, but now the names differenciate the wheat from the chaff.

Now, let’s make that same collection (still called SURFACE_OCEAN_MAGS) that doesn’t include SURFACE_OCEAN_Bin_00003 as a MAG, since the redundency is too high for what we want to look at right now.

anvi-rename-bins -c contigs-db \ -p profile-db \ --prefix SURFACE_OCEAN \ --collection-to-read MY_COLLECTION \ --collection-to-write SURFACE_OCEAN_MAGS \ --report-file rename.txt \ --min-completition-for-MAG 70 \ --max-redundancy-for-MAG 30 \ --call-MAGs

Now SURFACE_OCEAN_MAGS will include SURFACE_OCEAN_MAG_00001 SURFACE_OCEAN_MAG_00002, SURFACE_OCEAN_Bin_00003, and SURFACE_OCEAN_Bin_00004.

You also have the option to only classify bins above a certain minimum size as MAGs.

Example 3: An example use case in a workflow

For an example use case, on this page, anvi-rename-bins is used to create a new collection called MAGs that contains differenciates bins that have a completion stat of more than 70 percent, and renames all of those bins with the prefix IGD (which stands for infant gut dataset).

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.