internal-genomes [artifact]

A TXT-type anvi’o artifact. This artifact is typically provided by the user for anvi’o to import into its databases, process, and/or use.

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Provided by

There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.

Required or used by

anvi-compute-functional-enrichment anvi-compute-genome-similarity anvi-dereplicate-genomes anvi-estimate-metabolism anvi-gen-genomes-storage anvi-get-sequences-for-hmm-hits anvi-meta-pan-genome anvi-script-gen-hmm-hits-matrix-across-genomes

Description

An internal genome is any bin described in an anvi’o collection stored in an anvi’o profile-db. You can obtain one of these by binning a metagenome assembly (stored in an anvi’o contigs-db), which you can do either manually in the interactive interface or automatically with a binning software, and saving or importing it into a collection.

The internal genomes file format enables anvi’o to work with one or more bins from one or more collections that may be defined in different anvi’o profile-db files. A TAB-delimited internal genomes file will be composed of at least the following five columns:

name	bin_id	collection_id	profile_db_path	contigs_db_path
Name_01	Bin_id_01	Collection_A	/path/to/profile.db	/path/to/contigs.db
Name_02	Bin_id_02	Collection_A	/path/to/profile.db	/path/to/contigs.db
Name_03	Bin_id_03	Collection_B	/path/to/another_profile.db	/path/to/another/contigs.db
(…)	(…)	(…)	(…)	(…)

Please make sure names in the name column does not include any special characters (underscore is fine). It is also a good idea to keep these names short and descriptive as they will appear in various figures in downstream analyses.

Additional columns

In some cases additional columns may be required to be in this file. Below is a table of the possible columns you may need.

header	description	required for
group	name of the group that the genome belongs to (can be empty)	anvi-compute-functional-enrichment

Also see external-genomes and metagenomes.

Edit this file to update this information.