anvi-run-ncbi-cogs

This program runs NCBI's COGs to associate genes in an anvi'o contigs database with functions. This program can also run NCBI's COGs to annotate an amino acid sequence with function. COGs database was been designed as an attempt to classify proteins from completely sequenced genomes on the basis of the orthology concept..

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Authors

A. Murat Eren (Meren)
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Georges Kanaan (Gio)
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Requires

cogs-data contigs-db

Can use

fasta

Provides

functions

Can provide

functions-txt

Usage

This program annotates genes in your contigs-db with functions using NCBI’s Clusters of Orthologus Groups (COGs) database.

This program assumes that the user has successfully set up the COGs database on their computer using the anvi’o program anvi-setup-ncbi-cogs.

This program requires one of two possible inputs a contigs-db or a fasta file of amino acid sequences. When a contigs-db is provided, the program will store its output in the contigs-db as a functions artifact. Otherwise you must specify an output file path using -o, to which the program will write a TAB-delimited file containing all the annotatons found in the input fasta file.

If the cogs-data was stored at a specific path when anvi-setup-ncbi-cogs was run, then providing that path using the --cog-data-dir parameter is also necessary.

anvi-run-ncbi-cogs -c contigs-db \ --cog-data-dir path/to/cogs-data

Without the flag --cog-data-dir, anvi’o will just search in the default location.

Choosing a different database version

If you want to annotate your genes with a non-default version of cogs-data, provide that version after the --cog-version parameter:

anvi-setup-ncbi-cogs --cog-version COG24

Choosing a different search program

By default, this program uses diamond to search for hits to the database. You can also use blastp` to search, by running:

anvi-run-ncbi-cogs -c contigs-db \ --search-with blastp

Running with multiple threads

anvi-run-ncbi-cogs -c contigs-db \ --cog-data-dir path/to/cogs-data \ -T 16

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-run-ncbi-cogs.

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

anvi-run-ncbi-cogs [-h] [-c CONTIGS_DB] [-f FASTA file] [-o FILE_PATH] [--cog-version COG_VERSION] [--cog-data-dir COG_DATA_DIR] [-T NUM_THREADS] [--temporary-dir-path PATH] [--search-with SEARCH_METHOD]

Parameters and their descriptions

INPUT #1 - ANNOTATION OF CONTIGS DB One type of input this function can annotate is a contigs database. In this case anvi'o will attempt to annotate every gene present.
-c, --contigs-db CONTIGS_DB
Anvi'o contigs database generated by 'anvi-gen-contigs-database'
INPUT #2 - ANNOTATION OF FASTA FILE Another type of input this function can annotate is a FASTA file containing one or more amino acid sequences. In this case each gene sequence will be annotated and the functions will be reported as TAB-delimited output. In this mode you should specify an output file.
-f, --fasta-file FASTA FILE
A FASTA formatted input file containing protein sequences.
-o, --output-file FILE_PATH
File path to store results.
GENERAL OPTIONS These are general options which apply to both input modes.
--cog-version COG_VERSION
COG version. The default is the latest version, which is COG24, meaning that anvi'o will use the NCBI's 2024 release of COGs to setup the database and run it on contigs databases. Alternatively you can pass any of these as a parameter: 'COG20' (2020 release of the database), or 'COG14' (the 2014 release of the database). You can have multiple databases on your computer, and you can run multiple of them on a single contigs-db file. Cool and confusing. The anvi'o way.
--cog-data-dir COG_DATA_DIR
The directory path for your COG setup. Anvi'o will try to use the default path if you do not specify anything.
-T, --num-threads NUM_THREADS
Maximum number of threads to use for multithreading whenever possible. Very conservatively, the default is 1, unless the environmental variable `ANVIO_THREADS` sets another positive integer. If you use this parameter, it will override `ANVIO_THREADS`. It is a good idea to not exceed the number of CPUs / cores on your system. Plus, please be careful with this option if you are running your commands on a SGE -- if you are clusterizing your runs, and asking for multiple threads to use, you may deplete your resources very fast. Default: 1
--temporary-dir-path PATH
If you don't provide anything here, this program will come up with a temporary directory path by itself to store intermediate files, and clean it later. If you want to have full control over this, you can use this flag to define one.
--search-with SEARCH_METHOD
What program to use for database searching. The default search uses diamond. All available options include: diamond, blastp. Default: diamond

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.

Copyleft, The anvi'o Project