anvi-reaction-network
Table of Contents
This program generates a metabolic reaction network in an anvi'o contigs or pan database.
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Authors
Can consume
contigs-db 
kegg-functions 
reaction-ref-data kegg-data
Can provide
Usage
This program stores a metabolic reaction-network in a contigs-db or pan-db.
The network consists of data on biochemical reactions predicted to be encoded by the genome or pangenome.
Information on the predicted reactions and the involved metabolites are stored in tables of the contigs-db or pan-db. The program, anvi-get-metabolic-model-file, can be used to export the reaction-network from the database to a reaction-network-json file formatted for input into programs for flux balance analysis.
Setup
anvi-setup-kegg-data downloads, among other files, the binary relations files needed to construct a reaction-network from KEGG Orthology (KO) sequence annotations. The following command sets up the database in a default anvi’o directory.
anvi-setup-kegg-data
anvi-setup-modelseed-database sets up the ModelSEED Biochemistry database, which harmonizes biochemical data from various reference databases, including KEGG. The following command sets up the database in a default anvi’o directory.
anvi-setup-modelseed-database
Download newest available KEGG files
Alternatively, KEGG data can be set up not from a snapshot but by downloading the newest files available from KEGG using the -D flag. In the following command, a higher number of download threads than the default of 1 is provided by -T, which significantly speeds up downloading.
anvi-setup-kegg-data -D -T 5
Install in non-default location
To preserve KEGG data that you already have set up for whatever reason, the new snapshot or download can be placed in a non-default location using the option, --kegg-data-dir.
anvi-setup-kegg-data --kegg-data-dir path/to/other/directory
anvi-reaction-network requires a --kegg-dir argument to seek KEGG data in a non-default location.
Likewise, different versions of the ModelSEED Biochemistry database can be set up in non-default locations and used with the --modelseed-dir argument.
anvi-setup-modelseed-database --dir path/to/other/directory
Usage
anvi-reaction-network takes a either a contigs-db OR a pan-db and genomes-storage-db as required input. Genes stored within the contigs-db or genomes-storage-db must have KO protein annotations, which can be assigned by anvi-run-kegg-kofams.
anvi-reaction-network -c /path/to/contigs-db
If a contigs-db already contains a reaction-network from a previous run of this program, the flag --overwrite-existing-network can overwrite the existing network with a new one. For example, if anvi-run-kegg-kofams is run again on a database using a newer version of KEGG, then anvi-reaction-network should be rerun to update the reaction-network derived from the KO annotations.
anvi-reaction-network -c /path/to/contigs-db \ --overwrite-existing-network
A reaction-network can also be generated from consensus KO annotations of gene clusters. This can be used to understand the conservation or divergence of parts of the metabolic network between organisms in the pangenome.
anvi-reaction-network -p /path/to/pan-db \ -g /path/to/genomes-storage-db
Edit this file to update this information.
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.