anvi-script-gen-distribution-of-genes-in-a-bin

Quantify the detection of genes in genomes in metagenomes to identify the environmental core. This is a helper script for anvi'o metapangenomic workflow.

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Authors

A. Murat Eren (Meren)
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Requires

contigs-db profile-db

Can use

collection bin

Provides

view-data misc-data-items-txt

Usage

This program computes the detection of genes (inputted as a bin) across your samples, so that you can visualize them in the interactive interface.

This program is used in the metapangenomic workflow on genes with metagenomes as samples to visually identify the environmental core genes and accessory genes.

Inputs

Essentially, you provide a contigs-db and profile-db pair, as well as the bin you want to look at, and this program will search each gene in your bin against the samples denoted in your profile-db:

anvi-script-gen-distribution-of-genes-in-a-bin -c contigs-db \ -p profile-db \ -C collection \ -b bin

There are two other parameters that you can set to focus the genes that you’re looking at:

  • The minimum detection required for a gene to be included (by default, a gene must have a detection value of 0.5 in at least one of your samples) -The minimum coverage required for a gene to be included (by default, a gene must have a total coverage of 0.25 times the mean total coverage in your data)

Outputs

This program will produce two outputs:

  1. [your bin name]-GENE-COVs.txt, which is a view-data artifact. This is a matrix where each row represents a gene, each column represents one of your samples, and the cells each contain a coverage value.
  2. [your bin name]-ENV-DETECTION.txt, which is a misc-data-layers. It is a two-column file, where each row is a gene and and the second column describes whether or not that gene is systematically detected in your samples. Thus, this can be added as an additional layer in the interface that describes describes which genes are detected in your samples. (as an example, see the outermost layer here)

Thus, after running this program on a bin with name BIN_NAME, you can run

anvi-interactive -d BIN_NAME-GENE-COVs.txt \ -A BIN_NAME-ENV-DETECTION.txt \ --manual \ -p profile-db

This will visually show you the coverage and detection of your genes across your samples in the interactive interface (simlarly to this figure).

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-script-gen-distribution-of-genes-in-a-bin.

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-script-gen-distribution-of-genes-in-a-bin [-h] -c CONTIGS_DB [-p PROFILE_DB] [-C COLLECTION_NAME] [-b BIN_NAME] [--min-detection FLOAT] [--fraction-of-median-coverage FLOAT]

Parameters and their descriptions

options
-c, --contigs-db CONTIGS_DB required
Anvi'o contigs database generated by 'anvi-gen-contigs-database'
-p, --profile-db PROFILE_DB
Anvi'o profile database
-C, --collection-name COLLECTION_NAME
Collection name.
-b, --bin-id BIN_NAME
Bin name you are interested in.
--min-detection FLOAT
For this entire thing to work, the genome you are focusing on should be detected in at least one metagenome. If that is not the case, it would mean that you do not have any sample that represents the niche for this organism (or you do not have enough depth of coverage) to investigate the detection of genes in the environment. By default, this script requires at least '0.5' of the genome to be detected in at least one metagenome. This parameter allows you to change that. 0 would mean no detection test required, 1 would mean the entire genome must be detected. Default: 0.5
--fraction-of-median-coverage FLOAT
The value set here will be used to remove a gene if its total coverage across environments is less than the median coverage of all genes multiplied by this value. The default is 0.25, which means, if the median total coverage of all genes across all samples is 100X, then, a gene with a total coverage of less than 25X across all samples will be assumed not a part of the 'environmental core'. Default: 0.25

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