Microbial 'omics


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internal-genomes [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-compute-genome-similarity anvi-dereplicate-genomes anvi-estimate-metabolism anvi-gen-genomes-storage anvi-get-sequences-for-hmm-hits anvi-meta-pan-genome anvi-script-gen-hmm-hits-matrix-across-genomes

Description

An internal genome is any bin described in an anvi’o collection stored in an anvi’o profile-db.

The internal genomes file format enables anvi’o to work with one or more bins from one or more collections that may be defined in different anvi’o profile-db files. A TAB-delimited internal genomes file will be composed of the following five columns:

name bin_id collection_id profile_db_path contigs_db_path
Name_01 Bin_id_01 Collection_A /path/to/profile.db /path/to/contigs.db
Name_02 Bin_id_02 Collection_A /path/to/profile.db /path/to/contigs.db
Name_03 Bin_id_03 Collection_B /path/to/another_profile.db /path/to/another/contigs.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 external-genomes and metagenomes.

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