external-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-draw-kegg-pathways anvi-estimate-genome-completeness anvi-estimate-metabolism anvi-gen-genomes-storage anvi-get-codon-frequencies anvi-get-codon-usage-bias anvi-get-sequences-for-hmm-hits 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 external genome is any contigs-db generated from a FASTA file that describes a single genome for a single microbial population (and not a metagenome).

The purpose of the external genomes file is to describe one or more external genomes, so this file can be passed to anvi’o programs that can operate on multiple genomes.

For a given set of contigs-db files, you can generate an external-genomes file automatically using the program anvi-script-gen-genomes-file. Alternatively, you can manually create the file using a text editor, or a program like EXCEL.

The external-genomes file is a TAB-delimited file with at least two columns (you can add more columns to this file, and anvi’o will not mind):

• name. The name of the external genome. You can call it anything, but you should keep it to a single word witout any spaces or funny characters.
• contigs_db_path. The full path to each contigs-db file (tip: the command pwd will tell you the full path to the directory you are in).

The format of the file should look like this:

name	contigs_db_path
Name_01	/path/to/contigs-01.db
Name_02	/path/to/contigs-02.db
Name_03	/path/to/contigs-03.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 internal-genomes and metagenomes.

Edit this file to update this information.