Microbial 'omics


Brought to you by

metagenomes [artifact]

Table of Contents

TXT

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.

🔙 To the main page of anvi’o programs and artifacts.

Provided by

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.

Required or used by

anvi-estimate-metabolism anvi-estimate-scg-taxonomy anvi-estimate-trna-taxonomy

Description

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:

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
(…) (…)

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:

name contigs_db_path profile_db_path
Name_01 /path/to/contigs-01.db /path/to/profile.db
Name_02 /path/to/contigs-02.db /path/to/profile.db
Name_03 /path/to/contigs-03.db /path/to/profile.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 external-genomes.

Edit this file to update this information.