A COLLECTION-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
anvi-cluster-contigs anvi-delete-collection anvi-display-metabolism anvi-estimate-genome-completeness anvi-estimate-metabolism anvi-estimate-scg-taxonomy anvi-export-collection anvi-gen-gene-level-stats-databases anvi-get-aa-counts anvi-get-split-coverages anvi-merge-bins anvi-rename-bins anvi-split anvi-summarize anvi-script-gen-distribution-of-genes-in-a-bin
Essentially, a collection is a group of bins.
You can use collections to represent all kinds of things. The default collection (that you’ll get by running anvi-script-add-default-collection) is called DEFAULT and contains all of your contigs. However, you can put any group of bins into their own collection, and use that to limit what you’re analyzing downstream. A ton of anvi’o programs are able to take in a bin or a collection so that you don’t have to analyze your entire contigs-db when you just want to look at one section.
To look at the collections contained within an Anvi’o database, just run anvi-show-collections-and-bins. Or, to look at the completion estimates for all bins within a collection, use anvi-estimate-genome-completeness.
To view the content within a collection, use anvi-summarize.
Examples of collections in action
If your bins represent MAGs, you could use a collection to group related MAGs together. For example, you could group together genomes from the same population, or from the same taxonomic order. Or your could go even wider and have a collection for all of the Archaea genomes in your sample. You’re not limited by taxonomy either. You could go wild and have a collection for all of your bins that you suspect are prophages.
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