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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Required or used by
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.
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.
- a single genome, this table will contain a single line telling you the taxonomy estimate for your genome. It will also show the number of single-copy core genes or tRNA genes that support this estimate. If you run the
--debugflag, it will also display the hits for all of the single-copy core genes.
- a single metagenome, this table will list all of the hits for the chosen single-copy core gene or anticodon (by default, the one with the most hits) and their taxonomy information.
- a contigs-db and profile-db with the flag
--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.
- a collection, this table will show you each of your bins, and the best taxonomy estimate for each one, similarly to how it’s displayed for a run on a single genome.
- a metagenomes artifact, this table will give a gene entry ID, its taxonomy, and its corresponding coverage in your metagenomes. This format is essentially identical to the output for a single metagenome. If you provide the flag
--matrix-format, then it will list taxonomy information in each row, and tell you the coverage of each in each of your metagenomes.
Edit this file to update this information.