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, referencing the KEGG Orthology (KO) and ModelSEED Biochemistry databases.
Information on the predicted reactions and the involved metabolites are stored in two 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 flux balance analysis.
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.
The KO and ModelSEED Biochemistry databases must be set up and available to the program. By default, these are expected to be set up in default anvi’o data directories. anvi-setup-kegg-data and anvi-setup-modelseed-database must be run to set up these databases.
anvi-reaction-network -c /path/to/contigs-db
Custom locations for the reference databases can be provided with the flags, --ko-dir and --modelseed-dir.
anvi-reaction-network -c /path/to/contigs-db \ --ko-dir /path/to/set-up/ko-dir \ --modelseed-dir /path/to/set-up/modelseed-dir
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.