Merge multiple anvio profiles.
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The main function of
anvi-merge is to convert multiple single-profile-dbs into a single profile-db (also called a merged profile database). Basically, this takes the alignment data from each sample (each contained in its own single-profile-db) and combines them into a single database that anvi’o can look through more easily.
Set up your contigs-db. See that page for more information
Use anvi-profile to create a single-profile-db for each of your samples (formatted into a bam-file) (Note: for each of these runs, you’ll need to use the same contigs-db and parameters)
anvi-merge to merge those single-profile-dbs into a single database, called a profile-db. This will look something like the following:
anvi-merge -c cool_contigs.db \ Single_profile_db_1 Single_profile_db_2 \ -o cool_contigs_merge
This will put all of the output files (the final profile-db as well as a misc-data-items-order which is the result of your hierarchical clustering and describes the order to display your contigs in) into the folder
You must give
anvi-merge your contigs database and single profile databases. However, you can also provide more information or give addtional instructions. Use the flag
-h at any time to display the help menu.
--skip-hierarchical-clusteringto turn hierarchical clustering off. This will save on computation time, but will skip out on creating the tree of contigs at the center of the interactive interface. If you have more than 25,000 splits in the final profile, this will be set automatically.
--enforce-hierarchical-clusteringto turn hierarchical clustering back on. This will take a long time, but will produce a lovely contigs tree for the interactive interface.
--distance.(The default is euclidean)
--linkage.(The default is ward)
-S. If you don’t, anvi’o will come up with one, but it probably won’t be any good.
--description. This will show up when you later use the interactive interface to analyze your profile-db.
-Wto overwrite existing files in that directory.
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