Estimate completion and redundancy using domain-specific single-copy core genes.
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contigs-db profile-db external-genomes collection
This program estimates the completeness and redundancy of genomes provided to it, based on domain-level single-copy core genes.
Wondering what single-copy core genes anvi’o uses? Check out hmm-source. It uses the tables populated when you ran anvi-run-hmms on your contigs-db.
Genomes provided to this program must be contained in either a bin (within a collection) or a contigs-db (which can be provided alone or as part of an external-genomes).
For example, calling
anvi-estimate-genome-completeness -c contigs-db
will output to the terminal the completition and redundancy of the single-copy core genes in your contigs-db, assuming that all of its contigs represent a single genome. To output this information to a file, you can add the flag
-o and provide an output path.
To get this information for several contigs databases at once, you can provide them as an external-genomes, as so:
anvi-estimate-genome-completeness -e external-genomes \ -o completition.txt
To get this data for a series of bins, just provide a profile-db and collection.
anvi-estimate-genome-completeness -c contigs-db \ -p profile-db \ -C collection
To see what collections are contained in your contigs database, call
anvi-estimate-genome-completeness -c contigs-db \ -p profile-db \ --list-collections
or run anvi-show-collections-and-bins for a more comprehensive overview.
If you’re looking for a more comprehensive overview of your entire collection and its contents, the completition and redunduncy statistics for your bins are also included when you run anvi-summarize.
Edit this file to update this information.
Are you aware of resources that may help users better understand the utility of this program? Please feel free to edit this file on GitHub. If you are not sure how to do that, find the
__resources__ tag in this file to see an example.