anvi-rename-bins
Table of Contents
Rename all bins in a given collection (so they have pretty names).
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Usage
This program creates a new collection from the bins in another collection with specific guidelines. This is especially helpful when you wish to standardize your bin names, add project specific prefixes, and/or exclude those that do not match your criteria of completion, redundancy, and/or size estimates.
Renaming all bins in a collection
Let’s say you have a collection called MY_COLLECTION, which has four bins that are named poorly (which can happen due to decisions made by automatic binning tools, or after a few steps of manual refinement): Bin_1_2_1, Bin_2, Bin_3_1_1, and Bin_4. In an instance like this, running the program anvi-rename-bins the following way will standardize these bin names with a prefix specific to your project:
anvi-rename-bins -c contigs-db \ -p profile-db \ --prefix SURFACE_OCEAN \ --collection-to-read MY_COLLECTION \ --collection-to-write SURFACE_OCEAN_SAMPLES \ --report-file rename.txt
Now your profile-db will have a new collection named SURFACE_OCEAN_SAMPLES that will contains your four bins witht their new names SURFACE_OCEAN_Bin_00001, SURFACE_OCEAN_Bin_00002, SURFACE_OCEAN_Bin_00003, and SURFACE_OCEAN_Bin_00004. The new naming will order your bins based on their substantive completion (i.e., completion minus redunancy).
The file rename.txt is a TAB-delimited file that contains a summary of your renaming process. The first column has the original name of the bins that you renamed, the second has their new names, and the remaining columns contain information about those bins (like their completion, redundency, and size).
Separating out the MAGs
You can also label your MAGs separately from your bins via the flag --call-MAGs:
anvi-rename-bins -c contigs-db \ -p profile-db \ --prefix SURFACE_OCEAN \ --collection-to-read MY_COLLECTION \ --collection-to-write SURFACE_OCEAN_MAGS \ --report-file rename.txt \ --call-MAGs \ --min-completion-for-MAG 70
Now, the collection SURFACE_OCEAN_MAGS will include SURFACE_OCEAN_MAG_00001, SURFACE_OCEAN_MAG_00002, SURFACE_OCEAN_MAG_00003, and SURFACE_OCEAN_Bin_00004. These are exactly the same bins that the collection contained before, but now the names differenciate the wheat from the chaff.
In addition to minimum completion estimate, you can also adjust the maximum redundancy value, minimum size to call MAGs. Please see the help menu for all parameters and their descriptions.
Exclude bins that are not MAGs
When you use the flag --call-MAGs, anvi’o identifies those bins that could be considered ‘MAGs’ based on your specific criteria. But regardles of whether an original bin remains a bin, or tagged as a MAG, everything in your original collection will end up in your new collection. The flag --exclude-bins enable you to filter out those that end up not being tagged as MAGs:
anvi-rename-bins -c contigs-db \ -p profile-db \ --prefix SURFACE_OCEAN \ --collection-to-read MY_COLLECTION \ --collection-to-write SURFACE_OCEAN_MAGS \ --report-file rename.txt \ --min-completion-for-MAG 70 \ --call-MAGs \ --exclude-bins
With the addition of the flag --exclude-bins to the same command, the collection SURFACE_OCEAN_MAGS will no longer include bins SURFACE_OCEAN_Bin_00003 and SURFACE_OCEAN_Bin_00004.
See also the program anvi-delete-collection.
The report file
Following is an example reporting output file anvi’o will generate at the file path declared with the parameter --report-file:
| old_bin_name | new_bin_name | SCG_domain | completion | redundancy | size_in_Mbp |
|---|---|---|---|---|---|
| Bin_2 | p800_MAG_00001 | eukarya | 61.45 | 7.23 | 26.924911 |
| Bin_1 | p800_MAG_00002 | bacteria | 98.59 | 8.45 | 1.612349 |
| Bin_3 | p800_Bin_00003 | blank | 0.00 | 0.00 | 0.103694 |
| Bin_5 | p800_Bin_00004 | blank | 0.00 | 0.00 | 0.128382 |
| Bin_4 | p800_Bin_00005 | bacteria | 1.41 | 0.00 | 0.378418 |
The column SCG_domain will explain which collection of single-copy core genes were used to generate these completion/redundancy estimates. The absence of any domain prediction for any given bin will be marked with the keyrowd blank.
Edit this file to update this information.
Command line interface
The following is the list of parameters and their descriptions in the latest version of anvi-rename-bins.
The code that generates this web page ensures that this information is the latest available in 9-dev (eunice). Which means, in some cases the information in this section (generated automatically) might be more comprehensive or up-to-date compared to the descriptions above (written by humans).
Command line usage
Parameters and their descriptions
-c, --contigs-dbCONTIGS_DBrequired- Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-p, --profile-dbPROFILE_DBrequired- Anvi'o profile database
--collection-to-readCOLLECTION_TO_READ- Collection name to read from. Anvi'o will not overwrite an existing collection, instead, it will create a copy of your collection with new bin names.
--collection-to-writeCOLLECTION_TO_WRITE- The new collection name. Give it a nice, fancy name.
--prefixPREFIX- Prefix for the bin names. Must be a single word, composed of digits and numbers. The use of the underscore character is OK, but that's about it (fine, the use of the dash character is OK, too but no more!). If the prefix is 'PREFIX', each bin will be renamed as 'PREFIX_XXX_00001, PREFIX_XXX_00002', and so on, in the order of percent completion minus percent redundancy (what we call, 'substantive completion'). The 'XXX' part will either be 'Bin', or 'MAG depending on other parameters you use. Keep reading.
--report-fileREPORT_FILE_PATH- This file will report each name change event, so you can trace back the original names of renamed bins later.
--list-collections- Show available collections and exit.
--dry-run- When used does NOT update the profile database, just creates the report file so you can view how things will be renamed.
Additional Resources
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.