A CONCEPT-type anvi’o artifact. This artifact is typically generated, used, and/or exported by anvi’o (and not provided by the user)..
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There are no anvi’o tools that use or require this artifact directly, which means it is most likely an end-product for the user.
This artifact is the output tables that are displayed when you run anvi-estimate-scg-taxonomy or anvi-estimate-trna-taxonomy.
By default, they won’t be outputed anywhere, just displayed in the terminal for your viewing pleasure. If you want them in a tab-delimited file (as a genome-taxonomy-txt), just provide the
-o or the
-O prefix and anvi’o will do that for you.
The content of these tables will depend on how you ran anvi-estimate-trna-taxonomy or anvi-estimate-scg-taxonomy. This blog post gives you examples of what this looks like for each of the input scenarios for anvi-estimate-scg-taxonomy. Anvi-estimate-scg-taxonomy’s output is very similar, just with the results coming from different gene types. They will also be briefly described below.
When you run anvi-estimate-scg-taxonomy or anvi-estimate-scg-taxonomy on
--debugflag, it will also display the hits for all of the single-copy core genes.
--compute-scg-coverages, additional columns will be added that describe the coverage values for your single-copy core gene or tRNA gene hits across your samples.
--matrix-format, then it will list taxonomy information in each row, and tell you the coverage of each in each of your metagenomes.
This may sound confusing, but it is easier to understand when looking at the functionality of anvi-estimate-scg-taxonomy and the comprehensive examples given on this page.
Edit this file to update this information.