anvi-merge-bins

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Merge a given set of bins in an anvi'o collection.

🔙 To the main page of anvi’o programs and artifacts.

Authors

A. Murat Eren (Meren)

Requires

collection bin profile-db

Can use

pan-db

Provides

This program does not seem to provide any artifacts. Such programs usually print out some information for you to see or alter some anvi’o artifacts without producing any immediate outputs.

Usage

This program merges two or more bins together into a single bin.

To run this program, the bins that you want to merge must be contained within a single collection. Just provide the collection name, the pan-db or profile-db you’re working with, the bins that you want to merge, and the name of the output bin.

To check what collections and bins are contained in a database, you can either run this program with the flag --list-collections or --list-bins, or you can run anvi-show-collections-and-bins.

For example, if you wanted to merge the bins first_third, middle_third, and last_third in a pan-db into a single bin called complete_bin, just run

anvi-merge-bins -p pan-db \ -C collection \ -b first_third,middle_third,last_third \ -B complete_bin

Now your collection will contain the bin complete_bin and the original bins will be gone forever (unless you had runanvi-summarize, anvi-export-collection, or a similar program beforehand)

Edit this file to update this information.

Command line interface

The following is the list of parameters and their descriptions in the latest version of anvi-merge-bins.

The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).

Command line usage

anvi-merge-bins [-h] -p PAN_OR_PROFILE_DB [-C COLLECTION_NAME] [-b BIN NAMES] [-B BIN NAME] [--list-collections] [--list-bins]

Parameters and their descriptions

DB AND COLLECTION Simple enough. This guy needs a pan or profile database and a collection name. You can get a list of available collections with another flag down below.

-p, --pan-or-profile-db PAN_OR_PROFILE_DB required: An anvi'o pan-db or profile-db (and even genes-db or pan-graph-db in appropriate contexts).
-C, --collection-name COLLECTION_NAME: Collection name.

BINS TO WORK WITH Here you need to define a list of bin names to merge, and the new bin name for them to merge under. Your bin names should be comma-separated. Both 'name_1, name_2, name_3' and name_1,name_2,name_3 will work. Your new bin name better be a single word, meaningful name so anvi'o does not complain about it later.

-b, --bin-names-list BIN NAMES: Comma-separated list of bin names.
-B, --new-bin-name BIN NAME: The new bin name.

SWEET FLAGS OF CONVENIENCE We gotchu.

--list-collections: Show available collections and exit.
--list-bins: List available bins in a collection and exit.

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.