Microbial 'omics


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gene-taxonomy-txt [artifact]

Table of Contents

TXT

A TXT-type anvi’o artifact. This artifact can be generated, used, and/or exported by anvi’o. It can also be provided by the user for anvi’o to import into its databases, process, and/or use.

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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-import-taxonomy-for-genes

Description

This is a file containing the taxonomy information for the genes in your contigs-db.

You can use anvi-import-taxonomy-for-genes to integrate this information into your contigs database. See this blog post for a comprehensive tutorial.

In its simplest form, this file is a tab-delimited text file that lists gene caller IDs and their associated taxonomy information. However, anvi’o can also parse outputs from taxonomy-based software like Kaiju or Centrifuge.

For example:

gene_caller_id  t_domain     t_phylum       t_class      ...
      1         Eukarya      Chordata       Mammalia
      2         Prokarya     Bacteroidetes  Bacteroidia
      ...

Edit this file to update this information.