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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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
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:
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.
In some cases additional columns may be required to be in this file. Below is a table of the possible columns you may need.
|group||name of the group that the genome belongs to (can be empty)||anvi-compute-functional-enrichment|
Edit this file to update this information.