anvi-import-collection

Authors
Requires
Can use
Provides
Usage
Command line interface

Command line usage
Parameters and their descriptions

Additional Resources

Import an external binning result into anvi'o.

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

Authors

A. Murat Eren (Meren)

Requires

contigs-db collection-txt

Can use

profile-db pan-db pan-graph-db

Provides

collection

Usage

The purpose of this program is to import a collection into an anvi’o database.

The input to this program, a collection-txt, may either have been generated by another anvi’o program (such as anvi-export-collection), or may have been generated by the user manually. To import a collection into a database, you can run the following command,

anvi-import-collection collection-txt \ -p profile-db \ -c contigs-db \ -C COLLECTION_NAME

which would import the collection described in the input file formatted as a collection-txt into the profile-db with the name COLLECTION_NAME.

If your collection-txt describes contig names rather than split names, you will likely get an anvi’o error. You can fix that by adding the flag --contigs-mode to your command:

anvi-import-collection collection-txt \ -p profile-db \ -c contigs-db \ --contigs-mode \ -C COLLECTION_NAME

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-import-collection.

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-import-collection [-h] [--bins-info BINS_INFO] -C COLLECTION_NAME [-p PAN_OR_PROFILE_DB] [-c CONTIGS_DB] [--contigs-mode] TAB DELIMITED FILE

Parameters and their descriptions

INPUT DATA The input file that maps item names to bin names.

TAB DELIMITED FILE required: A two-column, tab-delimited file where column one has item names (splits, gene clusters, or synteny gene clusters) and column two has bin names.
--bins-info BINS_INFO: Additional information for bins. The file must contain three TAB-delimited columns, where the first one must be a unique bin name, the second should be a 'source', and the last one should be a 7 character HTML color code (i.e., '#424242'). Source column must contain information about the origin of the bin. If these bins are automatically identified by a program like CONCOCT, this column could contain the program name and version. The source information will be associated with the bin in various interfaces so in a sense it is not *that* critical what it says there, but on the other hand it is, becuse we should also think about people who may end up having to work with what we put together later.
-C, --collection-name COLLECTION_NAME required: Collection name.

TARGET DATABASE Where should the collection be stored?

-p, --pan-or-profile-db PAN_OR_PROFILE_DB: An anvi'o pan-db or profile-db (and even genes-db or pan-graph-db in appropriate contexts).
-c, --contigs-db CONTIGS_DB: Anvi'o contigs database generated by 'anvi-gen-contigs-database'

EXOTIC OPTIONS These parameters are only relevant when importing into a profile database associated with a contigs database and have no effect otherwise.

--contigs-mode: Use this flag if your binning was done on contigs instead of splits. Please refer to the documentation for help.

Additional Resources

Another description as part of the metagenomic workflow

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.