external-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


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-genome-completeness anvi-estimate-metabolism anvi-gen-genomes-storage anvi-get-sequences-for-hmm-hits anvi-script-gen-functions-per-group-stats-output anvi-script-gen-hmm-hits-matrix-across-genomes


An external genome is any genome assembly that was converted into a contigs-db from its original FASTA file format using the program anvi-gen-contigs-database. You can obtain one of these in a variety of ways, the most common being 1) downloading a genome from a database such as NCBI and 2) assembling a genome yourself from sequencing reads. The key thing is that the sequences in the contigs-db represent a single microbial population (or species, if you are not working with microbes) - ie, it is not a metagenome.

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 at least 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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