Microbial 'omics


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external-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.

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

Provided by

anvi-script-gen-genomes-file

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

Description

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.

Additional columns

In some cases additional columns may be required to be in this file. Below is a table of the possible columns you may need.

header description required for
group which group the genome belongs to (can be empty) anvi-compute-functional-enrichment

Also see internal-genomes and metagenomes.

Edit this file to update this information.