internal-genomes

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-codon-frequencies anvi-get-codon-usage-bias anvi-get-sequences-for-hmm-hits anvi-meta-pan-genome anvi-script-gen-function-matrix-across-genomes anvi-script-gen-functions-per-group-stats-output anvi-script-gen-hmm-hits-matrix-across-genomes

Description

In the anvi’o lingo, an internal genome is any bin stored in an anvi’o collection that describes a single genome. You can obtain one of these by binning a metagenome manually in the interactive interface, automatically using a binning software, or by importing a collection into anvi’o using the program anvi-import-collection.

The purpose of the external genomes file is to describe one or more internal genomes genomes, so this file can be passed to anvi’o programs that can operate on multiple genomes. The internal genomes file format enables anvi’o programs to work with one or more bins from one or more collections that may be defined in different anvi’o profile-db files.

The internal-genomes file is a TAB-delimited file with 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.