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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There are no anvi’o tools that generate this artifact, which means it is most likely provided to the anvi’o ecosystem by the user.
anvi-estimate-metabolism anvi-estimate-scg-taxonomy anvi-estimate-trna-taxonomy
A metagenome is any set of sequences that collectively describes multiple different populations (rather than just one genome) and has been converted into a contigs-db.
The metagenomes file format enables anvi’o to work with one or more metagenomes. A TAB-delimited external genomes file will be composed of at least the following two columns:
In some cases, (for example when running anvi-estimate-scg-taxonomy), you may also want to provide the profile-db that is associated with the contigs-db. Then the metagenomes file will be composed of three 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.
Also see internal-genomes and external-genomes.
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