In HUMAnN, it calculates the coverage of pathways from translated searching reads against a diamond database and then using MinPath.
In KEGG Maple (discontinued) and MicrobeAnnotator, it looks at KEGG Orthology then determines the completion for different KEGG modules such as bifurcated and structural modules. Basically, many of the pathways are complex and can't simply be 5/10 enzymes in the pathway are present.
What are open-sourced methods to calculate pathway coverage/completion from a set of enzymes?
I'm aware of PathwayTools but this requires licensing and is not open-sourced. I just tested out MinPath but it doesn't give me coverage/completion of pathways, just whether or not the pathway is present.
I am interested in MetaCyc, KEGG, BRENDA, and GO pathways/ontologies based on EC numbers.
