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

anvi-script-gen-genomes-file

Required or used by

anvi-compute-functional-enrichment-across-genomes anvi-compute-genome-similarity anvi-compute-metabolic-enrichment anvi-dereplicate-genomes anvi-display-functions anvi-estimate-metabolism anvi-gen-genomes-storage anvi-get-sequences-for-hmm-hits anvi-meta-pan-genome anvi-script-gen-functions-per-group-stats-output 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.

Also see external-genomes and metagenomes.

Edit this file to update this information.