Microbial 'omics


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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.

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Provided by

Most likely provided by the user.

Required or used by

anvi-estimate-metabolism anvi-estimate-scg-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.

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