Hello! Sorry if this question about concepts is a little basic, I am still a student.
One of Humann2 outputs is pathway coverage, which is dependent on reaction detection confidence (“a pathway with coverage = 1 is considered to be confidently detected, all of its member reactions were also confidently detected”). I also know, from other works, that there is a measure called completeness, which is the fraction of its genes that are present (100% completeness implies that all genes of the pathway are present).
Given that the presence of a reaction relies on the presence of genes, and that the presence of a gene requires its confident detection, which is the practical difference between pathway completeness and Humann2’s pathway coverage?
Thank you in advance.