Microbial 'omics

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external-genomes [artifact]

Table of Contents


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.

Back to the main page of anvi’o programs and artifacts.

Provided by

Most likely provided by the user.

Required or used by

anvi-compute-genome-similarity anvi-dereplicate-genomes anvi-estimate-genome-completeness anvi-estimate-metabolism anvi-gen-genomes-storage anvi-get-sequences-for-hmm-hits anvi-script-gen-hmm-hits-matrix-across-genomes


An external genome is anything you have in a FASTA file format (i.e., a genome you have downloaded from NCBI, or obtained through any other way) that was converted into a contigs-db.

The external genomes file format enables anvi’o to work with one or more external genomes. A TAB-delimited external genomes file will be composed of the following two columns:

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.

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